Package: xcmsAuthors: Johannes RainerModified: 2024-04-04 11:06:15.565571Compiled: Thu Apr 4 12:15:52 2024
Package: xcmsAuthors: Johannes RainerModified: 2024-04-16 06:54:18.520093Compiled: Tue Apr 16 08:07:41 2024
sessionInfo()
## R Under development (unstable) (2024-03-28 r86224) +## R Under development (unstable) (2024-04-10 r86396) ## Platform: x86_64-pc-linux-gnu ## Running under: Ubuntu 22.04.4 LTS ## @@ -843,63 +843,65 @@ Session information## ## other attached packages: ## [1] pheatmap_1.0.12 faahKO_1.43.0 MSnbase_2.29.4 -## [4] ProtGenerics_1.35.4 S4Vectors_0.41.5 mzR_2.37.3 +## [4] ProtGenerics_1.35.4 S4Vectors_0.41.6 mzR_2.37.3 ## [7] Rcpp_1.0.12 Biobase_2.63.1 BiocGenerics_0.49.1 -## [10] MsFeatures_1.11.0 xcms_4.1.12 BiocParallel_1.37.1 +## [10] MsFeatures_1.11.0 xcms_4.1.13 BiocParallel_1.37.1 ## [13] BiocStyle_2.31.0 ## ## loaded via a namespace (and not attached): ## [1] DBI_1.2.2 rlang_1.1.3 ## [3] magrittr_2.0.3 clue_0.3-65 -## [5] MassSpecWavelet_1.69.0 matrixStats_1.2.0 +## [5] MassSpecWavelet_1.69.0 matrixStats_1.3.0 ## [7] compiler_4.5.0 systemfonts_1.0.6 -## [9] vctrs_0.6.5 MetaboCoreUtils_1.11.2 +## [9] vctrs_0.6.5 MetaboCoreUtils_1.11.3 ## [11] pkgconfig_2.0.3 crayon_1.5.2 ## [13] fastmap_1.1.1 XVector_0.43.1 ## [15] utf8_1.2.4 rmarkdown_2.26 -## [17] preprocessCore_1.65.0 ragg_1.3.0 -## [19] purrr_1.0.2 xfun_0.43 -## [21] MultiAssayExperiment_1.29.1 zlibbioc_1.49.3 -## [23] cachem_1.0.8 GenomeInfoDb_1.39.10 -## [25] jsonlite_1.8.8 progress_1.2.3 -## [27] highr_0.10 DelayedArray_0.29.9 -## [29] prettyunits_1.2.0 parallel_4.5.0 -## [31] cluster_2.1.6 R6_2.5.1 -## [33] bslib_0.7.0 RColorBrewer_1.1-3 -## [35] limma_3.59.6 GenomicRanges_1.55.4 -## [37] jquerylib_0.1.4 bookdown_0.38 -## [39] SummarizedExperiment_1.33.3 iterators_1.0.14 -## [41] knitr_1.45 IRanges_2.37.1 -## [43] Matrix_1.7-0 igraph_2.0.3 -## [45] tidyselect_1.2.1 abind_1.4-5 -## [47] yaml_2.3.8 doParallel_1.0.17 -## [49] codetools_0.2-20 affy_1.81.0 -## [51] lattice_0.22-6 tibble_3.2.1 -## [53] plyr_1.8.9 evaluate_0.23 -## [55] desc_1.4.3 Spectra_1.13.8 -## [57] pillar_1.9.0 affyio_1.73.0 -## [59] BiocManager_1.30.22 MatrixGenerics_1.15.0 -## [61] foreach_1.5.2 MALDIquant_1.22.2 -## [63] ncdf4_1.22 generics_0.1.3 -## [65] hms_1.1.3 ggplot2_3.5.0 -## [67] munsell_0.5.1 scales_1.3.0 -## [69] MsExperiment_1.5.4 glue_1.7.0 -## [71] lazyeval_0.2.2 tools_4.5.0 -## [73] mzID_1.41.0 QFeatures_1.13.3 -## [75] vsn_3.71.1 fs_1.6.3 -## [77] XML_3.99-0.16.1 grid_4.5.0 -## [79] impute_1.77.0 MsCoreUtils_1.15.6 -## [81] colorspace_2.1-0 GenomeInfoDbData_1.2.12 -## [83] PSMatch_1.7.2 cli_3.6.2 -## [85] textshaping_0.3.7 fansi_1.0.6 -## [87] S4Arrays_1.3.6 dplyr_1.1.4 -## [89] AnnotationFilter_1.27.0 pcaMethods_1.95.0 -## [91] gtable_0.3.4 sass_0.4.9 -## [93] digest_0.6.35 SparseArray_1.3.4 -## [95] farver_2.1.1 htmlwidgets_1.6.4 -## [97] memoise_2.0.1 htmltools_0.5.8.1 -## [99] pkgdown_2.0.7.9000 lifecycle_1.0.4 -## [101] statmod_1.5.0 MASS_7.3-60.2 +## [17] UCSC.utils_0.99.5 preprocessCore_1.65.0 +## [19] ragg_1.3.0 purrr_1.0.2 +## [21] xfun_0.43 MultiAssayExperiment_1.29.1 +## [23] zlibbioc_1.49.3 cachem_1.0.8 +## [25] GenomeInfoDb_1.39.13 jsonlite_1.8.8 +## [27] progress_1.2.3 highr_0.10 +## [29] DelayedArray_0.29.9 prettyunits_1.2.0 +## [31] parallel_4.5.0 cluster_2.1.6 +## [33] R6_2.5.1 bslib_0.7.0 +## [35] RColorBrewer_1.1-3 limma_3.59.8 +## [37] GenomicRanges_1.55.4 jquerylib_0.1.4 +## [39] iterators_1.0.14 bookdown_0.39 +## [41] SummarizedExperiment_1.33.3 knitr_1.46 +## [43] IRanges_2.37.1 Matrix_1.7-0 +## [45] igraph_2.0.3 tidyselect_1.2.1 +## [47] abind_1.4-5 yaml_2.3.8 +## [49] doParallel_1.0.17 codetools_0.2-20 +## [51] affy_1.81.0 lattice_0.22-6 +## [53] tibble_3.2.1 plyr_1.8.9 +## [55] evaluate_0.23 desc_1.4.3 +## [57] Spectra_1.13.8 pillar_1.9.0 +## [59] affyio_1.73.0 BiocManager_1.30.22 +## [61] MatrixGenerics_1.15.0 foreach_1.5.2 +## [63] MALDIquant_1.22.2 ncdf4_1.22 +## [65] generics_0.1.3 hms_1.1.3 +## [67] ggplot2_3.5.0 munsell_0.5.1 +## [69] scales_1.3.0 MsExperiment_1.5.4 +## [71] glue_1.7.0 lazyeval_0.2.2 +## [73] tools_4.5.0 mzID_1.41.0 +## [75] QFeatures_1.13.7 vsn_3.71.1 +## [77] fs_1.6.3 XML_3.99-0.16.1 +## [79] grid_4.5.0 impute_1.77.0 +## [81] tidyr_1.3.1 MsCoreUtils_1.15.6 +## [83] colorspace_2.1-0 GenomeInfoDbData_1.2.12 +## [85] PSMatch_1.7.2 cli_3.6.2 +## [87] textshaping_0.3.7 fansi_1.0.6 +## [89] S4Arrays_1.3.7 dplyr_1.1.4 +## [91] AnnotationFilter_1.27.0 pcaMethods_1.95.0 +## [93] gtable_0.3.4 sass_0.4.9 +## [95] digest_0.6.35 SparseArray_1.3.5 +## [97] farver_2.1.1 htmlwidgets_1.6.4 +## [99] memoise_2.0.1 htmltools_0.5.8.1 +## [101] pkgdown_2.0.8.9000 lifecycle_1.0.4 +## [103] httr_1.4.7 statmod_1.5.0 +## [105] MASS_7.3-60.2
## R Under development (unstable) (2024-04-10 r86396) ## Platform: x86_64-pc-linux-gnu ## Running under: Ubuntu 22.04.4 LTS ## @@ -843,63 +843,65 @@ Session information## ## other attached packages: ## [1] pheatmap_1.0.12 faahKO_1.43.0 MSnbase_2.29.4 -## [4] ProtGenerics_1.35.4 S4Vectors_0.41.5 mzR_2.37.3 +## [4] ProtGenerics_1.35.4 S4Vectors_0.41.6 mzR_2.37.3 ## [7] Rcpp_1.0.12 Biobase_2.63.1 BiocGenerics_0.49.1 -## [10] MsFeatures_1.11.0 xcms_4.1.12 BiocParallel_1.37.1 +## [10] MsFeatures_1.11.0 xcms_4.1.13 BiocParallel_1.37.1 ## [13] BiocStyle_2.31.0 ## ## loaded via a namespace (and not attached): ## [1] DBI_1.2.2 rlang_1.1.3 ## [3] magrittr_2.0.3 clue_0.3-65 -## [5] MassSpecWavelet_1.69.0 matrixStats_1.2.0 +## [5] MassSpecWavelet_1.69.0 matrixStats_1.3.0 ## [7] compiler_4.5.0 systemfonts_1.0.6 -## [9] vctrs_0.6.5 MetaboCoreUtils_1.11.2 +## [9] vctrs_0.6.5 MetaboCoreUtils_1.11.3 ## [11] pkgconfig_2.0.3 crayon_1.5.2 ## [13] fastmap_1.1.1 XVector_0.43.1 ## [15] utf8_1.2.4 rmarkdown_2.26 -## [17] preprocessCore_1.65.0 ragg_1.3.0 -## [19] purrr_1.0.2 xfun_0.43 -## [21] MultiAssayExperiment_1.29.1 zlibbioc_1.49.3 -## [23] cachem_1.0.8 GenomeInfoDb_1.39.10 -## [25] jsonlite_1.8.8 progress_1.2.3 -## [27] highr_0.10 DelayedArray_0.29.9 -## [29] prettyunits_1.2.0 parallel_4.5.0 -## [31] cluster_2.1.6 R6_2.5.1 -## [33] bslib_0.7.0 RColorBrewer_1.1-3 -## [35] limma_3.59.6 GenomicRanges_1.55.4 -## [37] jquerylib_0.1.4 bookdown_0.38 -## [39] SummarizedExperiment_1.33.3 iterators_1.0.14 -## [41] knitr_1.45 IRanges_2.37.1 -## [43] Matrix_1.7-0 igraph_2.0.3 -## [45] tidyselect_1.2.1 abind_1.4-5 -## [47] yaml_2.3.8 doParallel_1.0.17 -## [49] codetools_0.2-20 affy_1.81.0 -## [51] lattice_0.22-6 tibble_3.2.1 -## [53] plyr_1.8.9 evaluate_0.23 -## [55] desc_1.4.3 Spectra_1.13.8 -## [57] pillar_1.9.0 affyio_1.73.0 -## [59] BiocManager_1.30.22 MatrixGenerics_1.15.0 -## [61] foreach_1.5.2 MALDIquant_1.22.2 -## [63] ncdf4_1.22 generics_0.1.3 -## [65] hms_1.1.3 ggplot2_3.5.0 -## [67] munsell_0.5.1 scales_1.3.0 -## [69] MsExperiment_1.5.4 glue_1.7.0 -## [71] lazyeval_0.2.2 tools_4.5.0 -## [73] mzID_1.41.0 QFeatures_1.13.3 -## [75] vsn_3.71.1 fs_1.6.3 -## [77] XML_3.99-0.16.1 grid_4.5.0 -## [79] impute_1.77.0 MsCoreUtils_1.15.6 -## [81] colorspace_2.1-0 GenomeInfoDbData_1.2.12 -## [83] PSMatch_1.7.2 cli_3.6.2 -## [85] textshaping_0.3.7 fansi_1.0.6 -## [87] S4Arrays_1.3.6 dplyr_1.1.4 -## [89] AnnotationFilter_1.27.0 pcaMethods_1.95.0 -## [91] gtable_0.3.4 sass_0.4.9 -## [93] digest_0.6.35 SparseArray_1.3.4 -## [95] farver_2.1.1 htmlwidgets_1.6.4 -## [97] memoise_2.0.1 htmltools_0.5.8.1 -## [99] pkgdown_2.0.7.9000 lifecycle_1.0.4 -## [101] statmod_1.5.0 MASS_7.3-60.2
Site built with pkgdown 2.0.7.9000.
Site built with pkgdown 2.0.8.9000.
## R Under development (unstable) (2024-03-28 r86224) +## R Under development (unstable) (2024-04-10 r86396) ## Platform: x86_64-pc-linux-gnu ## Running under: Ubuntu 22.04.4 LTS ## @@ -458,63 +458,65 @@ Session information## [8] base ## ## other attached packages: -## [1] MassSpecWavelet_1.69.0 xcms_4.1.12 BiocParallel_1.37.1 -## [4] MSnbase_2.29.4 ProtGenerics_1.35.4 S4Vectors_0.41.5 +## [1] MassSpecWavelet_1.69.0 xcms_4.1.13 BiocParallel_1.37.1 +## [4] MSnbase_2.29.4 ProtGenerics_1.35.4 S4Vectors_0.41.6 ## [7] mzR_2.37.3 Rcpp_1.0.12 Biobase_2.63.1 ## [10] BiocGenerics_0.49.1 BiocStyle_2.31.0 ## ## loaded via a namespace (and not attached): ## [1] DBI_1.2.2 rlang_1.1.3 ## [3] magrittr_2.0.3 clue_0.3-65 -## [5] matrixStats_1.2.0 compiler_4.5.0 +## [5] matrixStats_1.3.0 compiler_4.5.0 ## [7] systemfonts_1.0.6 vctrs_0.6.5 -## [9] MetaboCoreUtils_1.11.2 pkgconfig_2.0.3 +## [9] MetaboCoreUtils_1.11.3 pkgconfig_2.0.3 ## [11] crayon_1.5.2 fastmap_1.1.1 ## [13] XVector_0.43.1 utf8_1.2.4 -## [15] rmarkdown_2.26 preprocessCore_1.65.0 -## [17] ragg_1.3.0 purrr_1.0.2 -## [19] xfun_0.43 MultiAssayExperiment_1.29.1 -## [21] zlibbioc_1.49.3 cachem_1.0.8 -## [23] GenomeInfoDb_1.39.10 jsonlite_1.8.8 -## [25] progress_1.2.3 highr_0.10 -## [27] DelayedArray_0.29.9 prettyunits_1.2.0 -## [29] parallel_4.5.0 cluster_2.1.6 -## [31] R6_2.5.1 RColorBrewer_1.1-3 -## [33] bslib_0.7.0 limma_3.59.6 -## [35] GenomicRanges_1.55.4 jquerylib_0.1.4 -## [37] bookdown_0.38 SummarizedExperiment_1.33.3 -## [39] iterators_1.0.14 knitr_1.45 -## [41] IRanges_2.37.1 Matrix_1.7-0 -## [43] igraph_2.0.3 tidyselect_1.2.1 -## [45] abind_1.4-5 yaml_2.3.8 -## [47] doParallel_1.0.17 codetools_0.2-20 -## [49] affy_1.81.0 lattice_0.22-6 -## [51] tibble_3.2.1 plyr_1.8.9 -## [53] signal_1.8-0 evaluate_0.23 -## [55] desc_1.4.3 Spectra_1.13.8 -## [57] pillar_1.9.0 affyio_1.73.0 -## [59] BiocManager_1.30.22 MatrixGenerics_1.15.0 -## [61] foreach_1.5.2 MALDIquant_1.22.2 -## [63] ncdf4_1.22 generics_0.1.3 -## [65] hms_1.1.3 ggplot2_3.5.0 -## [67] munsell_0.5.1 scales_1.3.0 -## [69] MsExperiment_1.5.4 glue_1.7.0 -## [71] MsFeatures_1.11.0 lazyeval_0.2.2 -## [73] tools_4.5.0 mzID_1.41.0 -## [75] QFeatures_1.13.3 vsn_3.71.1 -## [77] fs_1.6.3 XML_3.99-0.16.1 -## [79] grid_4.5.0 impute_1.77.0 -## [81] MsCoreUtils_1.15.6 colorspace_2.1-0 -## [83] GenomeInfoDbData_1.2.12 PSMatch_1.7.2 -## [85] cli_3.6.2 textshaping_0.3.7 -## [87] fansi_1.0.6 S4Arrays_1.3.6 -## [89] dplyr_1.1.4 AnnotationFilter_1.27.0 -## [91] pcaMethods_1.95.0 gtable_0.3.4 -## [93] sass_0.4.9 digest_0.6.35 -## [95] SparseArray_1.3.4 htmlwidgets_1.6.4 -## [97] memoise_2.0.1 htmltools_0.5.8.1 -## [99] pkgdown_2.0.7.9000 lifecycle_1.0.4 -## [101] statmod_1.5.0 MASS_7.3-60.2 +## [15] rmarkdown_2.26 UCSC.utils_0.99.5 +## [17] preprocessCore_1.65.0 ragg_1.3.0 +## [19] purrr_1.0.2 xfun_0.43 +## [21] MultiAssayExperiment_1.29.1 zlibbioc_1.49.3 +## [23] cachem_1.0.8 GenomeInfoDb_1.39.13 +## [25] jsonlite_1.8.8 progress_1.2.3 +## [27] highr_0.10 DelayedArray_0.29.9 +## [29] prettyunits_1.2.0 parallel_4.5.0 +## [31] cluster_2.1.6 R6_2.5.1 +## [33] RColorBrewer_1.1-3 bslib_0.7.0 +## [35] limma_3.59.8 GenomicRanges_1.55.4 +## [37] jquerylib_0.1.4 bookdown_0.39 +## [39] SummarizedExperiment_1.33.3 iterators_1.0.14 +## [41] knitr_1.46 IRanges_2.37.1 +## [43] Matrix_1.7-0 igraph_2.0.3 +## [45] tidyselect_1.2.1 abind_1.4-5 +## [47] yaml_2.3.8 doParallel_1.0.17 +## [49] codetools_0.2-20 affy_1.81.0 +## [51] lattice_0.22-6 tibble_3.2.1 +## [53] plyr_1.8.9 signal_1.8-0 +## [55] evaluate_0.23 desc_1.4.3 +## [57] Spectra_1.13.8 pillar_1.9.0 +## [59] affyio_1.73.0 BiocManager_1.30.22 +## [61] MatrixGenerics_1.15.0 foreach_1.5.2 +## [63] MALDIquant_1.22.2 ncdf4_1.22 +## [65] generics_0.1.3 hms_1.1.3 +## [67] ggplot2_3.5.0 munsell_0.5.1 +## [69] scales_1.3.0 MsExperiment_1.5.4 +## [71] glue_1.7.0 MsFeatures_1.11.0 +## [73] lazyeval_0.2.2 tools_4.5.0 +## [75] mzID_1.41.0 QFeatures_1.13.7 +## [77] vsn_3.71.1 fs_1.6.3 +## [79] XML_3.99-0.16.1 grid_4.5.0 +## [81] impute_1.77.0 tidyr_1.3.1 +## [83] MsCoreUtils_1.15.6 colorspace_2.1-0 +## [85] GenomeInfoDbData_1.2.12 PSMatch_1.7.2 +## [87] cli_3.6.2 textshaping_0.3.7 +## [89] fansi_1.0.6 S4Arrays_1.3.7 +## [91] dplyr_1.1.4 AnnotationFilter_1.27.0 +## [93] pcaMethods_1.95.0 gtable_0.3.4 +## [95] sass_0.4.9 digest_0.6.35 +## [97] SparseArray_1.3.5 htmlwidgets_1.6.4 +## [99] memoise_2.0.1 htmltools_0.5.8.1 +## [101] pkgdown_2.0.8.9000 lifecycle_1.0.4 +## [103] httr_1.4.7 statmod_1.5.0 +## [105] MASS_7.3-60.2
## R Under development (unstable) (2024-04-10 r86396) ## Platform: x86_64-pc-linux-gnu ## Running under: Ubuntu 22.04.4 LTS ## @@ -458,63 +458,65 @@ Session information## [8] base ## ## other attached packages: -## [1] MassSpecWavelet_1.69.0 xcms_4.1.12 BiocParallel_1.37.1 -## [4] MSnbase_2.29.4 ProtGenerics_1.35.4 S4Vectors_0.41.5 +## [1] MassSpecWavelet_1.69.0 xcms_4.1.13 BiocParallel_1.37.1 +## [4] MSnbase_2.29.4 ProtGenerics_1.35.4 S4Vectors_0.41.6 ## [7] mzR_2.37.3 Rcpp_1.0.12 Biobase_2.63.1 ## [10] BiocGenerics_0.49.1 BiocStyle_2.31.0 ## ## loaded via a namespace (and not attached): ## [1] DBI_1.2.2 rlang_1.1.3 ## [3] magrittr_2.0.3 clue_0.3-65 -## [5] matrixStats_1.2.0 compiler_4.5.0 +## [5] matrixStats_1.3.0 compiler_4.5.0 ## [7] systemfonts_1.0.6 vctrs_0.6.5 -## [9] MetaboCoreUtils_1.11.2 pkgconfig_2.0.3 +## [9] MetaboCoreUtils_1.11.3 pkgconfig_2.0.3 ## [11] crayon_1.5.2 fastmap_1.1.1 ## [13] XVector_0.43.1 utf8_1.2.4 -## [15] rmarkdown_2.26 preprocessCore_1.65.0 -## [17] ragg_1.3.0 purrr_1.0.2 -## [19] xfun_0.43 MultiAssayExperiment_1.29.1 -## [21] zlibbioc_1.49.3 cachem_1.0.8 -## [23] GenomeInfoDb_1.39.10 jsonlite_1.8.8 -## [25] progress_1.2.3 highr_0.10 -## [27] DelayedArray_0.29.9 prettyunits_1.2.0 -## [29] parallel_4.5.0 cluster_2.1.6 -## [31] R6_2.5.1 RColorBrewer_1.1-3 -## [33] bslib_0.7.0 limma_3.59.6 -## [35] GenomicRanges_1.55.4 jquerylib_0.1.4 -## [37] bookdown_0.38 SummarizedExperiment_1.33.3 -## [39] iterators_1.0.14 knitr_1.45 -## [41] IRanges_2.37.1 Matrix_1.7-0 -## [43] igraph_2.0.3 tidyselect_1.2.1 -## [45] abind_1.4-5 yaml_2.3.8 -## [47] doParallel_1.0.17 codetools_0.2-20 -## [49] affy_1.81.0 lattice_0.22-6 -## [51] tibble_3.2.1 plyr_1.8.9 -## [53] signal_1.8-0 evaluate_0.23 -## [55] desc_1.4.3 Spectra_1.13.8 -## [57] pillar_1.9.0 affyio_1.73.0 -## [59] BiocManager_1.30.22 MatrixGenerics_1.15.0 -## [61] foreach_1.5.2 MALDIquant_1.22.2 -## [63] ncdf4_1.22 generics_0.1.3 -## [65] hms_1.1.3 ggplot2_3.5.0 -## [67] munsell_0.5.1 scales_1.3.0 -## [69] MsExperiment_1.5.4 glue_1.7.0 -## [71] MsFeatures_1.11.0 lazyeval_0.2.2 -## [73] tools_4.5.0 mzID_1.41.0 -## [75] QFeatures_1.13.3 vsn_3.71.1 -## [77] fs_1.6.3 XML_3.99-0.16.1 -## [79] grid_4.5.0 impute_1.77.0 -## [81] MsCoreUtils_1.15.6 colorspace_2.1-0 -## [83] GenomeInfoDbData_1.2.12 PSMatch_1.7.2 -## [85] cli_3.6.2 textshaping_0.3.7 -## [87] fansi_1.0.6 S4Arrays_1.3.6 -## [89] dplyr_1.1.4 AnnotationFilter_1.27.0 -## [91] pcaMethods_1.95.0 gtable_0.3.4 -## [93] sass_0.4.9 digest_0.6.35 -## [95] SparseArray_1.3.4 htmlwidgets_1.6.4 -## [97] memoise_2.0.1 htmltools_0.5.8.1 -## [99] pkgdown_2.0.7.9000 lifecycle_1.0.4 -## [101] statmod_1.5.0 MASS_7.3-60.2
Package: xcmsAuthors: Johannes Rainer, Michael WittingModified: 2024-04-04 11:06:15.565571Compiled: Thu Apr 4 12:16:52 2024
Package: xcmsAuthors: Johannes Rainer, Michael WittingModified: 2024-04-16 06:54:18.520093Compiled: Tue Apr 16 08:08:38 2024
By default chromPeakSpectra returns all spectra associated with a MS1 chromatographic peak, but parameter method allows to choose and return only one spectrum per @@ -343,9 +343,9 @@
chromPeakSpectra
method
There are 5 MS2 spectra representing fragmentation of the ion(s) measured in our candidate chromatographic peak. We next reduce this to a single MS2 spectrum using the combineSpectra method @@ -371,9 +371,9 @@
combineSpectra
Mass peaks from all input spectra with a difference in m/z smaller 20 ppm (parameter ppm) were combined into one peak and the @@ -832,7 +832,7 @@
ppm
As a result we got a Spectra object of length equal to the number of MS1 peaks in our data. The length of a spectrum represents the number of peaks it contains. Thus, a length of 0 indicates that no @@ -994,9 +994,9 @@
Spectra
In total 5 spectra were measured, some with a relatively high number of peaks. Next we combine them into a consensus spectrum.
@@ -1133,7 +1133,7 @@ Session information sessionInfo()
## R Under development (unstable) (2024-03-28 r86224) +## R Under development (unstable) (2024-04-10 r86396) ## Platform: x86_64-pc-linux-gnu ## Running under: Ubuntu 22.04.4 LTS ## @@ -1157,64 +1157,65 @@ Session information## [8] base ## ## other attached packages: -## [1] MetaboCoreUtils_1.11.2 MsBackendMgf_1.11.2 MsExperiment_1.5.4 +## [1] MetaboCoreUtils_1.11.3 MsBackendMgf_1.11.2 MsExperiment_1.5.4 ## [4] pander_0.6.5 Spectra_1.13.8 ProtGenerics_1.35.4 -## [7] S4Vectors_0.41.5 BiocGenerics_0.49.1 xcms_4.1.12 +## [7] S4Vectors_0.41.6 BiocGenerics_0.49.1 xcms_4.1.13 ## [10] BiocParallel_1.37.1 BiocStyle_2.31.0 ## ## loaded via a namespace (and not attached): ## [1] DBI_1.2.2 rlang_1.1.3 ## [3] magrittr_2.0.3 clue_0.3-65 -## [5] MassSpecWavelet_1.69.0 matrixStats_1.2.0 +## [5] MassSpecWavelet_1.69.0 matrixStats_1.3.0 ## [7] compiler_4.5.0 systemfonts_1.0.6 ## [9] vctrs_0.6.5 pkgconfig_2.0.3 ## [11] crayon_1.5.2 fastmap_1.1.1 ## [13] XVector_0.43.1 utf8_1.2.4 -## [15] rmarkdown_2.26 preprocessCore_1.65.0 -## [17] ragg_1.3.0 purrr_1.0.2 -## [19] xfun_0.43 MultiAssayExperiment_1.29.1 -## [21] zlibbioc_1.49.3 cachem_1.0.8 -## [23] GenomeInfoDb_1.39.10 jsonlite_1.8.8 -## [25] progress_1.2.3 highr_0.10 -## [27] DelayedArray_0.29.9 prettyunits_1.2.0 -## [29] parallel_4.5.0 cluster_2.1.6 -## [31] R6_2.5.1 bslib_0.7.0 -## [33] RColorBrewer_1.1-3 limma_3.59.6 -## [35] GenomicRanges_1.55.4 jquerylib_0.1.4 -## [37] Rcpp_1.0.12 bookdown_0.38 -## [39] SummarizedExperiment_1.33.3 iterators_1.0.14 -## [41] knitr_1.45 IRanges_2.37.1 -## [43] Matrix_1.7-0 igraph_2.0.3 -## [45] tidyselect_1.2.1 abind_1.4-5 -## [47] yaml_2.3.8 doParallel_1.0.17 -## [49] codetools_0.2-20 affy_1.81.0 -## [51] lattice_0.22-6 tibble_3.2.1 -## [53] plyr_1.8.9 Biobase_2.63.1 -## [55] evaluate_0.23 desc_1.4.3 -## [57] pillar_1.9.0 affyio_1.73.0 -## [59] BiocManager_1.30.22 MatrixGenerics_1.15.0 -## [61] foreach_1.5.2 MSnbase_2.29.4 -## [63] MALDIquant_1.22.2 ncdf4_1.22 -## [65] generics_0.1.3 hms_1.1.3 -## [67] ggplot2_3.5.0 munsell_0.5.1 -## [69] scales_1.3.0 glue_1.7.0 -## [71] MsFeatures_1.11.0 lazyeval_0.2.2 -## [73] tools_4.5.0 mzID_1.41.0 -## [75] QFeatures_1.13.3 vsn_3.71.1 -## [77] mzR_2.37.3 fs_1.6.3 -## [79] XML_3.99-0.16.1 grid_4.5.0 -## [81] impute_1.77.0 MsCoreUtils_1.15.6 -## [83] colorspace_2.1-0 GenomeInfoDbData_1.2.12 -## [85] PSMatch_1.7.2 cli_3.6.2 -## [87] textshaping_0.3.7 fansi_1.0.6 -## [89] S4Arrays_1.3.6 dplyr_1.1.4 -## [91] AnnotationFilter_1.27.0 pcaMethods_1.95.0 -## [93] gtable_0.3.4 sass_0.4.9 -## [95] digest_0.6.35 SparseArray_1.3.4 -## [97] htmlwidgets_1.6.4 memoise_2.0.1 -## [99] htmltools_0.5.8.1 pkgdown_2.0.7.9000 -## [101] lifecycle_1.0.4 statmod_1.5.0 -## [103] MASS_7.3-60.2 +## [15] rmarkdown_2.26 UCSC.utils_0.99.5 +## [17] preprocessCore_1.65.0 ragg_1.3.0 +## [19] purrr_1.0.2 xfun_0.43 +## [21] MultiAssayExperiment_1.29.1 zlibbioc_1.49.3 +## [23] cachem_1.0.8 GenomeInfoDb_1.39.13 +## [25] jsonlite_1.8.8 progress_1.2.3 +## [27] highr_0.10 DelayedArray_0.29.9 +## [29] prettyunits_1.2.0 parallel_4.5.0 +## [31] cluster_2.1.6 R6_2.5.1 +## [33] bslib_0.7.0 RColorBrewer_1.1-3 +## [35] limma_3.59.8 GenomicRanges_1.55.4 +## [37] jquerylib_0.1.4 iterators_1.0.14 +## [39] Rcpp_1.0.12 bookdown_0.39 +## [41] SummarizedExperiment_1.33.3 knitr_1.46 +## [43] IRanges_2.37.1 Matrix_1.7-0 +## [45] igraph_2.0.3 tidyselect_1.2.1 +## [47] abind_1.4-5 yaml_2.3.8 +## [49] doParallel_1.0.17 codetools_0.2-20 +## [51] affy_1.81.0 lattice_0.22-6 +## [53] tibble_3.2.1 plyr_1.8.9 +## [55] Biobase_2.63.1 evaluate_0.23 +## [57] desc_1.4.3 pillar_1.9.0 +## [59] affyio_1.73.0 BiocManager_1.30.22 +## [61] MatrixGenerics_1.15.0 foreach_1.5.2 +## [63] MSnbase_2.29.4 MALDIquant_1.22.2 +## [65] ncdf4_1.22 generics_0.1.3 +## [67] hms_1.1.3 ggplot2_3.5.0 +## [69] munsell_0.5.1 scales_1.3.0 +## [71] glue_1.7.0 MsFeatures_1.11.0 +## [73] lazyeval_0.2.2 tools_4.5.0 +## [75] mzID_1.41.0 QFeatures_1.13.7 +## [77] vsn_3.71.1 mzR_2.37.3 +## [79] fs_1.6.3 XML_3.99-0.16.1 +## [81] grid_4.5.0 impute_1.77.0 +## [83] tidyr_1.3.1 MsCoreUtils_1.15.6 +## [85] colorspace_2.1-0 GenomeInfoDbData_1.2.12 +## [87] PSMatch_1.7.2 cli_3.6.2 +## [89] textshaping_0.3.7 fansi_1.0.6 +## [91] S4Arrays_1.3.7 dplyr_1.1.4 +## [93] AnnotationFilter_1.27.0 pcaMethods_1.95.0 +## [95] gtable_0.3.4 sass_0.4.9 +## [97] digest_0.6.35 SparseArray_1.3.5 +## [99] htmlwidgets_1.6.4 memoise_2.0.1 +## [101] htmltools_0.5.8.1 pkgdown_2.0.8.9000 +## [103] lifecycle_1.0.4 httr_1.4.7 +## [105] statmod_1.5.0 MASS_7.3-60.2
## R Under development (unstable) (2024-04-10 r86396) ## Platform: x86_64-pc-linux-gnu ## Running under: Ubuntu 22.04.4 LTS ## @@ -1157,64 +1157,65 @@ Session information## [8] base ## ## other attached packages: -## [1] MetaboCoreUtils_1.11.2 MsBackendMgf_1.11.2 MsExperiment_1.5.4 +## [1] MetaboCoreUtils_1.11.3 MsBackendMgf_1.11.2 MsExperiment_1.5.4 ## [4] pander_0.6.5 Spectra_1.13.8 ProtGenerics_1.35.4 -## [7] S4Vectors_0.41.5 BiocGenerics_0.49.1 xcms_4.1.12 +## [7] S4Vectors_0.41.6 BiocGenerics_0.49.1 xcms_4.1.13 ## [10] BiocParallel_1.37.1 BiocStyle_2.31.0 ## ## loaded via a namespace (and not attached): ## [1] DBI_1.2.2 rlang_1.1.3 ## [3] magrittr_2.0.3 clue_0.3-65 -## [5] MassSpecWavelet_1.69.0 matrixStats_1.2.0 +## [5] MassSpecWavelet_1.69.0 matrixStats_1.3.0 ## [7] compiler_4.5.0 systemfonts_1.0.6 ## [9] vctrs_0.6.5 pkgconfig_2.0.3 ## [11] crayon_1.5.2 fastmap_1.1.1 ## [13] XVector_0.43.1 utf8_1.2.4 -## [15] rmarkdown_2.26 preprocessCore_1.65.0 -## [17] ragg_1.3.0 purrr_1.0.2 -## [19] xfun_0.43 MultiAssayExperiment_1.29.1 -## [21] zlibbioc_1.49.3 cachem_1.0.8 -## [23] GenomeInfoDb_1.39.10 jsonlite_1.8.8 -## [25] progress_1.2.3 highr_0.10 -## [27] DelayedArray_0.29.9 prettyunits_1.2.0 -## [29] parallel_4.5.0 cluster_2.1.6 -## [31] R6_2.5.1 bslib_0.7.0 -## [33] RColorBrewer_1.1-3 limma_3.59.6 -## [35] GenomicRanges_1.55.4 jquerylib_0.1.4 -## [37] Rcpp_1.0.12 bookdown_0.38 -## [39] SummarizedExperiment_1.33.3 iterators_1.0.14 -## [41] knitr_1.45 IRanges_2.37.1 -## [43] Matrix_1.7-0 igraph_2.0.3 -## [45] tidyselect_1.2.1 abind_1.4-5 -## [47] yaml_2.3.8 doParallel_1.0.17 -## [49] codetools_0.2-20 affy_1.81.0 -## [51] lattice_0.22-6 tibble_3.2.1 -## [53] plyr_1.8.9 Biobase_2.63.1 -## [55] evaluate_0.23 desc_1.4.3 -## [57] pillar_1.9.0 affyio_1.73.0 -## [59] BiocManager_1.30.22 MatrixGenerics_1.15.0 -## [61] foreach_1.5.2 MSnbase_2.29.4 -## [63] MALDIquant_1.22.2 ncdf4_1.22 -## [65] generics_0.1.3 hms_1.1.3 -## [67] ggplot2_3.5.0 munsell_0.5.1 -## [69] scales_1.3.0 glue_1.7.0 -## [71] MsFeatures_1.11.0 lazyeval_0.2.2 -## [73] tools_4.5.0 mzID_1.41.0 -## [75] QFeatures_1.13.3 vsn_3.71.1 -## [77] mzR_2.37.3 fs_1.6.3 -## [79] XML_3.99-0.16.1 grid_4.5.0 -## [81] impute_1.77.0 MsCoreUtils_1.15.6 -## [83] colorspace_2.1-0 GenomeInfoDbData_1.2.12 -## [85] PSMatch_1.7.2 cli_3.6.2 -## [87] textshaping_0.3.7 fansi_1.0.6 -## [89] S4Arrays_1.3.6 dplyr_1.1.4 -## [91] AnnotationFilter_1.27.0 pcaMethods_1.95.0 -## [93] gtable_0.3.4 sass_0.4.9 -## [95] digest_0.6.35 SparseArray_1.3.4 -## [97] htmlwidgets_1.6.4 memoise_2.0.1 -## [99] htmltools_0.5.8.1 pkgdown_2.0.7.9000 -## [101] lifecycle_1.0.4 statmod_1.5.0 -## [103] MASS_7.3-60.2
Package: xcmsAuthors: Johannes RainerModified: 2024-04-04 11:06:15.565571Compiled: Thu Apr 4 12:17:27 2024
Package: xcmsAuthors: Johannes RainerModified: 2024-04-16 06:54:18.524093Compiled: Tue Apr 16 08:09:13 2024
## Object of class "XProcessHistory" ## type: Peak detection -## date: Thu Apr 4 12:18:02 2024 +## date: Tue Apr 16 08:09:47 2024 ## info: ## fileIndex: 1,2,3,4,5,6,7,8 ## Parameter class: CentWaveParam @@ -2202,7 +2202,7 @@ Session information sessionInfo() -## R Under development (unstable) (2024-03-28 r86224) +## R Under development (unstable) (2024-04-10 r86396) ## Platform: x86_64-pc-linux-gnu ## Running under: Ubuntu 22.04.4 LTS ## @@ -2227,65 +2227,67 @@ Session information## ## other attached packages: ## [1] SummarizedExperiment_1.33.3 Biobase_2.63.1 -## [3] GenomicRanges_1.55.4 GenomeInfoDb_1.39.10 -## [5] IRanges_2.37.1 S4Vectors_0.41.5 +## [3] GenomicRanges_1.55.4 GenomeInfoDb_1.39.13 +## [5] IRanges_2.37.1 S4Vectors_0.41.6 ## [7] BiocGenerics_0.49.1 MatrixGenerics_1.15.0 -## [9] matrixStats_1.2.0 MsExperiment_1.5.4 +## [9] matrixStats_1.3.0 MsExperiment_1.5.4 ## [11] ProtGenerics_1.35.4 pheatmap_1.0.12 ## [13] RColorBrewer_1.1-3 pander_0.6.5 -## [15] faahKO_1.43.0 xcms_4.1.12 +## [15] faahKO_1.43.0 xcms_4.1.13 ## [17] BiocParallel_1.37.1 BiocStyle_2.31.0 ## ## loaded via a namespace (and not attached): -## [1] DBI_1.2.2 rlang_1.1.3 -## [3] magrittr_2.0.3 clue_0.3-65 -## [5] MassSpecWavelet_1.69.0 compiler_4.5.0 -## [7] systemfonts_1.0.6 vctrs_0.6.5 -## [9] MetaboCoreUtils_1.11.2 pkgconfig_2.0.3 -## [11] crayon_1.5.2 fastmap_1.1.1 -## [13] XVector_0.43.1 utf8_1.2.4 -## [15] rmarkdown_2.26 preprocessCore_1.65.0 -## [17] ragg_1.3.0 purrr_1.0.2 -## [19] xfun_0.43 MultiAssayExperiment_1.29.1 -## [21] zlibbioc_1.49.3 cachem_1.0.8 -## [23] jsonlite_1.8.8 progress_1.2.3 -## [25] highr_0.10 DelayedArray_0.29.9 -## [27] prettyunits_1.2.0 parallel_4.5.0 -## [29] cluster_2.1.6 R6_2.5.1 -## [31] bslib_0.7.0 limma_3.59.6 -## [33] jquerylib_0.1.4 Rcpp_1.0.12 -## [35] bookdown_0.38 iterators_1.0.14 -## [37] knitr_1.45 Matrix_1.7-0 -## [39] igraph_2.0.3 tidyselect_1.2.1 -## [41] abind_1.4-5 yaml_2.3.8 -## [43] doParallel_1.0.17 codetools_0.2-20 -## [45] affy_1.81.0 lattice_0.22-6 -## [47] tibble_3.2.1 plyr_1.8.9 -## [49] evaluate_0.23 desc_1.4.3 -## [51] Spectra_1.13.8 pillar_1.9.0 -## [53] affyio_1.73.0 BiocManager_1.30.22 -## [55] foreach_1.5.2 MSnbase_2.29.4 -## [57] MALDIquant_1.22.2 ncdf4_1.22 -## [59] generics_0.1.3 hms_1.1.3 -## [61] ggplot2_3.5.0 munsell_0.5.1 -## [63] scales_1.3.0 glue_1.7.0 -## [65] MsFeatures_1.11.0 lazyeval_0.2.2 -## [67] tools_4.5.0 mzID_1.41.0 -## [69] QFeatures_1.13.3 vsn_3.71.1 -## [71] mzR_2.37.3 fs_1.6.3 -## [73] XML_3.99-0.16.1 grid_4.5.0 -## [75] impute_1.77.0 MsCoreUtils_1.15.6 -## [77] colorspace_2.1-0 GenomeInfoDbData_1.2.12 -## [79] PSMatch_1.7.2 cli_3.6.2 -## [81] textshaping_0.3.7 fansi_1.0.6 -## [83] S4Arrays_1.3.6 dplyr_1.1.4 -## [85] AnnotationFilter_1.27.0 pcaMethods_1.95.0 -## [87] gtable_0.3.4 sass_0.4.9 -## [89] digest_0.6.35 SparseArray_1.3.4 -## [91] farver_2.1.1 htmlwidgets_1.6.4 -## [93] memoise_2.0.1 htmltools_0.5.8.1 -## [95] pkgdown_2.0.7.9000 lifecycle_1.0.4 -## [97] statmod_1.5.0 MASS_7.3-60.2 +## [1] DBI_1.2.2 rlang_1.1.3 +## [3] magrittr_2.0.3 clue_0.3-65 +## [5] MassSpecWavelet_1.69.0 compiler_4.5.0 +## [7] systemfonts_1.0.6 vctrs_0.6.5 +## [9] MetaboCoreUtils_1.11.3 pkgconfig_2.0.3 +## [11] crayon_1.5.2 fastmap_1.1.1 +## [13] XVector_0.43.1 utf8_1.2.4 +## [15] rmarkdown_2.26 UCSC.utils_0.99.5 +## [17] preprocessCore_1.65.0 ragg_1.3.0 +## [19] purrr_1.0.2 xfun_0.43 +## [21] MultiAssayExperiment_1.29.1 zlibbioc_1.49.3 +## [23] cachem_1.0.8 jsonlite_1.8.8 +## [25] progress_1.2.3 highr_0.10 +## [27] DelayedArray_0.29.9 prettyunits_1.2.0 +## [29] parallel_4.5.0 cluster_2.1.6 +## [31] R6_2.5.1 bslib_0.7.0 +## [33] limma_3.59.8 jquerylib_0.1.4 +## [35] iterators_1.0.14 Rcpp_1.0.12 +## [37] bookdown_0.39 knitr_1.46 +## [39] Matrix_1.7-0 igraph_2.0.3 +## [41] tidyselect_1.2.1 abind_1.4-5 +## [43] yaml_2.3.8 doParallel_1.0.17 +## [45] codetools_0.2-20 affy_1.81.0 +## [47] lattice_0.22-6 tibble_3.2.1 +## [49] plyr_1.8.9 evaluate_0.23 +## [51] desc_1.4.3 Spectra_1.13.8 +## [53] pillar_1.9.0 affyio_1.73.0 +## [55] BiocManager_1.30.22 foreach_1.5.2 +## [57] MSnbase_2.29.4 MALDIquant_1.22.2 +## [59] ncdf4_1.22 generics_0.1.3 +## [61] hms_1.1.3 ggplot2_3.5.0 +## [63] munsell_0.5.1 scales_1.3.0 +## [65] glue_1.7.0 MsFeatures_1.11.0 +## [67] lazyeval_0.2.2 tools_4.5.0 +## [69] mzID_1.41.0 QFeatures_1.13.7 +## [71] vsn_3.71.1 mzR_2.37.3 +## [73] fs_1.6.3 XML_3.99-0.16.1 +## [75] grid_4.5.0 impute_1.77.0 +## [77] tidyr_1.3.1 MsCoreUtils_1.15.6 +## [79] colorspace_2.1-0 GenomeInfoDbData_1.2.12 +## [81] PSMatch_1.7.2 cli_3.6.2 +## [83] textshaping_0.3.7 fansi_1.0.6 +## [85] S4Arrays_1.3.7 dplyr_1.1.4 +## [87] AnnotationFilter_1.27.0 pcaMethods_1.95.0 +## [89] gtable_0.3.4 sass_0.4.9 +## [91] digest_0.6.35 SparseArray_1.3.5 +## [93] farver_2.1.1 htmlwidgets_1.6.4 +## [95] memoise_2.0.1 htmltools_0.5.8.1 +## [97] pkgdown_2.0.8.9000 lifecycle_1.0.4 +## [99] httr_1.4.7 statmod_1.5.0 +## [101] MASS_7.3-60.2 References @@ -2351,7 +2353,7 @@ References -Site built with pkgdown 2.0.7.9000. +Site built with pkgdown 2.0.8.9000. diff --git a/authors.html b/authors.html index 212d9555..17de0959 100644 --- a/authors.html +++ b/authors.html @@ -10,7 +10,7 @@ xcms - 4.1.12 + 4.1.13 @@ -144,7 +144,7 @@ Citation diff --git a/favicon-16x16.png b/favicon-16x16.png index 53c982c0..3044290e 100644 Binary files a/favicon-16x16.png and b/favicon-16x16.png differ diff --git a/favicon-32x32.png b/favicon-32x32.png index 851800a5..68d96750 100644 Binary files a/favicon-32x32.png and b/favicon-32x32.png differ diff --git a/index.html b/index.html index 0a6e1c28..e1bec737 100644 --- a/index.html +++ b/index.html @@ -33,7 +33,7 @@ xcms - 4.1.12 + 4.1.13 @@ -197,7 +197,7 @@ Dev status diff --git a/news/index.html b/news/index.html index b6e9296d..121e3e26 100644 --- a/news/index.html +++ b/news/index.html @@ -10,7 +10,7 @@ xcms - 4.1.12 + 4.1.13 @@ -58,35 +58,39 @@ xcms 4.1 -Changes in version 4.1.12 +Changes in version 4.1.13 +Add parameter rtimeDifferenceThreshold to ObiwarpParam allowing to customize the threshold used by obiwarp to determine whether gaps are present in the sequence of retention times of a sample. This addresses/fixes issue #739. + + +Changes in version 4.1.12 Implementation of the LamaParama class and method for the adjustRtime() function. Allowing alignment of a dataset based on landmarks (lamas) from an external reference dataset. Implementation of related user-level function matchLamasChromPeaks(), summarizeMatchLama() and plot(LamaParama) which allows for evaluation of matching between lamas and chromPeaks. -Changes in version 4.1.11 +Changes in version 4.1.11 Clean up of required and suggested packages and namespace imports. Re-creation of bundled data objects. -Changes in version 4.1.10 +Changes in version 4.1.10 Ensure backward compatibility for parameter objects that gained additional slots. -Changes in version 4.1.9 +Changes in version 4.1.9 Fix bug in filterFeatures,PercentMissingFilter. -Changes in version 4.1.8 +Changes in version 4.1.8 Fixing issue #716: edit of .empty_chrom_peaks function so an sn column is returned. Fixes extracting and plotting of peaks after using manualChromPeaks -Changes in version 4.1.7 +Changes in version 4.1.7 Implementation of filterFeatures function with filter parameters: RsdFilter, DratioFilter, PercentMissingFilter, BlankFlag. They can be used ot filter features from XcmsResult and SummarizedExperiment objects. Addition of a section in the main xcms vignette to describe how to use it. -Changes in version 4.1.6 +Changes in version 4.1.6 Import filterSpectra from MsExperiment. Import breaks_ppm from MsCoreUtils. Update featureArea function to consider all chromatographic peaks per feature, not only the one with the highest intensity. As a consequence, returned m/z and rt ranges might be higher which has an influence in featureChromatograms, EIC-based feature grouping and, to a lesser extent also in gap-filling. Related documentation was updated. @@ -94,13 +98,13 @@ Changes in version 4.1.6Add parameter ppm to PeakDensityParam to enable peak-density-based correspondence throgh m/z-dependent bins along the m/z. -Changes in version 4.1.5 +Changes in version 4.1.5 Improve performance of the chromatogram call for XcmsExperiment objects. Remove internal (not exported) normalization functions. These have been transferred to the MetaboCoreUtils package. Support subsetting of XcmsExperiment with negative indices. -Changes in version 4.1.4 +Changes in version 4.1.4 Rename variable data in the vignette to faahko. Fix issue in adjustRtime resulting in corrupt processHistory. Add support to perform peakGroups alignment using pre-defined anchor peak matrix (i.e., the numeric matrix with retention times of anchor peaks in the samples that can be used to align these samples). @@ -110,15 +114,15 @@ Changes in version 4.1.4Ensure chunk-wise processing of Spectra (introduced with version 1.13.2) is disabled when xcms is using its own chunk-wise processing. -Changes in version 4.1.3 +Changes in version 4.1.3 Add parameter verboseBetaColumns to CentWaveParam to enable calculation of additional peak quality metrics comparing the EIC to an idealized bell curve. -Changes in version 4.1.2 +Changes in version 4.1.2 Add a param = to generic function storeResults: PlainTextParam to save an XcmsExperiment or MsExperiment object as colleciton of plain text files. -Changes in version 4.1.1 +Changes in version 4.1.1 Add method storeResults and one of its param =: RDataParam to save an XcmsExperiment object as an .RData file. @@ -1041,7 +1045,7 @@ CHANGED BEHAVIOUR since Version diff --git a/pkgdown.yml b/pkgdown.yml index 32ef7313..0ce0e7c3 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -1,12 +1,12 @@ pandoc: 3.1.1 -pkgdown: 2.0.7.9000 -pkgdown_sha: 9b928b2bab23a8f450787d260c77eae848db1561 +pkgdown: 2.0.8.9000 +pkgdown_sha: d139e038a1ddb7b7696a435aac0798dea2c3ce44 articles: LC-MS-feature-grouping: LC-MS-feature-grouping.html xcms-direct-injection: xcms-direct-injection.html xcms-lcms-ms: xcms-lcms-ms.html xcms: xcms.html -last_built: 2024-04-04T12:13Z +last_built: 2024-04-16T08:05Z urls: reference: https://sneumann.github.io/xcms/reference article: https://sneumann.github.io/xcms/articles diff --git a/reference/AutoLockMass-methods.html b/reference/AutoLockMass-methods.html index 25e4e107..8cdcc526 100644 --- a/reference/AutoLockMass-methods.html +++ b/reference/AutoLockMass-methods.html @@ -12,7 +12,7 @@ xcms - 4.1.12 + 4.1.13 @@ -136,7 +136,7 @@ Examples - Site built with pkgdown 2.0.7.9000. + Site built with pkgdown 2.0.8.9000. diff --git a/reference/BlankFlag.html b/reference/BlankFlag.html index 4ebce59c..7dd456b3 100644 --- a/reference/BlankFlag.html +++ b/reference/BlankFlag.html @@ -28,7 +28,7 @@ xcms - 4.1.12 + 4.1.13 @@ -186,7 +186,7 @@ Author< diff --git a/reference/DratioFilter.html b/reference/DratioFilter.html index 3ba52ffa..7d37eea2 100644 --- a/reference/DratioFilter.html +++ b/reference/DratioFilter.html @@ -24,7 +24,7 @@ xcms - 4.1.12 + 4.1.13 @@ -190,7 +190,7 @@ Author< diff --git a/reference/GenericParam.html b/reference/GenericParam.html index 768c1012..35da5c22 100644 --- a/reference/GenericParam.html +++ b/reference/GenericParam.html @@ -22,7 +22,7 @@ xcms - 4.1.12 + 4.1.13 @@ -142,7 +142,7 @@ Examples - Site built with pkgdown 2.0.7.9000. + Site built with pkgdown 2.0.8.9000. diff --git a/reference/LamaParama.html b/reference/LamaParama.html index b95ee76f..14c57fa0 100644 --- a/reference/LamaParama.html +++ b/reference/LamaParama.html @@ -84,7 +84,7 @@ xcms - 4.1.12 + 4.1.13 @@ -397,7 +397,7 @@ Examples - Site built with pkgdown 2.0.7.9000. + Site built with pkgdown 2.0.8.9000. diff --git a/reference/PercentMissingFilter.html b/reference/PercentMissingFilter.html index 03e73f56..53cf0e29 100644 --- a/reference/PercentMissingFilter.html +++ b/reference/PercentMissingFilter.html @@ -26,7 +26,7 @@ xcms - 4.1.12 + 4.1.13 @@ -165,7 +165,7 @@ Author< diff --git a/reference/PlainTextParam.html b/reference/PlainTextParam.html index 36067186..038b625b 100644 --- a/reference/PlainTextParam.html +++ b/reference/PlainTextParam.html @@ -76,7 +76,7 @@ xcms - 4.1.12 + 4.1.13 @@ -234,7 +234,7 @@ Examples ## Save as a collection of plain text files storeResults(object = faahko_sub, param = param) -#> Warning: '/tmp/RtmpujIEHL/test' already exists +#> Warning: '/tmp/RtmpDb4oE7/test' already exists
## R Under development (unstable) (2024-03-28 r86224) +## R Under development (unstable) (2024-04-10 r86396) ## Platform: x86_64-pc-linux-gnu ## Running under: Ubuntu 22.04.4 LTS ## @@ -2227,65 +2227,67 @@ Session information## ## other attached packages: ## [1] SummarizedExperiment_1.33.3 Biobase_2.63.1 -## [3] GenomicRanges_1.55.4 GenomeInfoDb_1.39.10 -## [5] IRanges_2.37.1 S4Vectors_0.41.5 +## [3] GenomicRanges_1.55.4 GenomeInfoDb_1.39.13 +## [5] IRanges_2.37.1 S4Vectors_0.41.6 ## [7] BiocGenerics_0.49.1 MatrixGenerics_1.15.0 -## [9] matrixStats_1.2.0 MsExperiment_1.5.4 +## [9] matrixStats_1.3.0 MsExperiment_1.5.4 ## [11] ProtGenerics_1.35.4 pheatmap_1.0.12 ## [13] RColorBrewer_1.1-3 pander_0.6.5 -## [15] faahKO_1.43.0 xcms_4.1.12 +## [15] faahKO_1.43.0 xcms_4.1.13 ## [17] BiocParallel_1.37.1 BiocStyle_2.31.0 ## ## loaded via a namespace (and not attached): -## [1] DBI_1.2.2 rlang_1.1.3 -## [3] magrittr_2.0.3 clue_0.3-65 -## [5] MassSpecWavelet_1.69.0 compiler_4.5.0 -## [7] systemfonts_1.0.6 vctrs_0.6.5 -## [9] MetaboCoreUtils_1.11.2 pkgconfig_2.0.3 -## [11] crayon_1.5.2 fastmap_1.1.1 -## [13] XVector_0.43.1 utf8_1.2.4 -## [15] rmarkdown_2.26 preprocessCore_1.65.0 -## [17] ragg_1.3.0 purrr_1.0.2 -## [19] xfun_0.43 MultiAssayExperiment_1.29.1 -## [21] zlibbioc_1.49.3 cachem_1.0.8 -## [23] jsonlite_1.8.8 progress_1.2.3 -## [25] highr_0.10 DelayedArray_0.29.9 -## [27] prettyunits_1.2.0 parallel_4.5.0 -## [29] cluster_2.1.6 R6_2.5.1 -## [31] bslib_0.7.0 limma_3.59.6 -## [33] jquerylib_0.1.4 Rcpp_1.0.12 -## [35] bookdown_0.38 iterators_1.0.14 -## [37] knitr_1.45 Matrix_1.7-0 -## [39] igraph_2.0.3 tidyselect_1.2.1 -## [41] abind_1.4-5 yaml_2.3.8 -## [43] doParallel_1.0.17 codetools_0.2-20 -## [45] affy_1.81.0 lattice_0.22-6 -## [47] tibble_3.2.1 plyr_1.8.9 -## [49] evaluate_0.23 desc_1.4.3 -## [51] Spectra_1.13.8 pillar_1.9.0 -## [53] affyio_1.73.0 BiocManager_1.30.22 -## [55] foreach_1.5.2 MSnbase_2.29.4 -## [57] MALDIquant_1.22.2 ncdf4_1.22 -## [59] generics_0.1.3 hms_1.1.3 -## [61] ggplot2_3.5.0 munsell_0.5.1 -## [63] scales_1.3.0 glue_1.7.0 -## [65] MsFeatures_1.11.0 lazyeval_0.2.2 -## [67] tools_4.5.0 mzID_1.41.0 -## [69] QFeatures_1.13.3 vsn_3.71.1 -## [71] mzR_2.37.3 fs_1.6.3 -## [73] XML_3.99-0.16.1 grid_4.5.0 -## [75] impute_1.77.0 MsCoreUtils_1.15.6 -## [77] colorspace_2.1-0 GenomeInfoDbData_1.2.12 -## [79] PSMatch_1.7.2 cli_3.6.2 -## [81] textshaping_0.3.7 fansi_1.0.6 -## [83] S4Arrays_1.3.6 dplyr_1.1.4 -## [85] AnnotationFilter_1.27.0 pcaMethods_1.95.0 -## [87] gtable_0.3.4 sass_0.4.9 -## [89] digest_0.6.35 SparseArray_1.3.4 -## [91] farver_2.1.1 htmlwidgets_1.6.4 -## [93] memoise_2.0.1 htmltools_0.5.8.1 -## [95] pkgdown_2.0.7.9000 lifecycle_1.0.4 -## [97] statmod_1.5.0 MASS_7.3-60.2 +## [1] DBI_1.2.2 rlang_1.1.3 +## [3] magrittr_2.0.3 clue_0.3-65 +## [5] MassSpecWavelet_1.69.0 compiler_4.5.0 +## [7] systemfonts_1.0.6 vctrs_0.6.5 +## [9] MetaboCoreUtils_1.11.3 pkgconfig_2.0.3 +## [11] crayon_1.5.2 fastmap_1.1.1 +## [13] XVector_0.43.1 utf8_1.2.4 +## [15] rmarkdown_2.26 UCSC.utils_0.99.5 +## [17] preprocessCore_1.65.0 ragg_1.3.0 +## [19] purrr_1.0.2 xfun_0.43 +## [21] MultiAssayExperiment_1.29.1 zlibbioc_1.49.3 +## [23] cachem_1.0.8 jsonlite_1.8.8 +## [25] progress_1.2.3 highr_0.10 +## [27] DelayedArray_0.29.9 prettyunits_1.2.0 +## [29] parallel_4.5.0 cluster_2.1.6 +## [31] R6_2.5.1 bslib_0.7.0 +## [33] limma_3.59.8 jquerylib_0.1.4 +## [35] iterators_1.0.14 Rcpp_1.0.12 +## [37] bookdown_0.39 knitr_1.46 +## [39] Matrix_1.7-0 igraph_2.0.3 +## [41] tidyselect_1.2.1 abind_1.4-5 +## [43] yaml_2.3.8 doParallel_1.0.17 +## [45] codetools_0.2-20 affy_1.81.0 +## [47] lattice_0.22-6 tibble_3.2.1 +## [49] plyr_1.8.9 evaluate_0.23 +## [51] desc_1.4.3 Spectra_1.13.8 +## [53] pillar_1.9.0 affyio_1.73.0 +## [55] BiocManager_1.30.22 foreach_1.5.2 +## [57] MSnbase_2.29.4 MALDIquant_1.22.2 +## [59] ncdf4_1.22 generics_0.1.3 +## [61] hms_1.1.3 ggplot2_3.5.0 +## [63] munsell_0.5.1 scales_1.3.0 +## [65] glue_1.7.0 MsFeatures_1.11.0 +## [67] lazyeval_0.2.2 tools_4.5.0 +## [69] mzID_1.41.0 QFeatures_1.13.7 +## [71] vsn_3.71.1 mzR_2.37.3 +## [73] fs_1.6.3 XML_3.99-0.16.1 +## [75] grid_4.5.0 impute_1.77.0 +## [77] tidyr_1.3.1 MsCoreUtils_1.15.6 +## [79] colorspace_2.1-0 GenomeInfoDbData_1.2.12 +## [81] PSMatch_1.7.2 cli_3.6.2 +## [83] textshaping_0.3.7 fansi_1.0.6 +## [85] S4Arrays_1.3.7 dplyr_1.1.4 +## [87] AnnotationFilter_1.27.0 pcaMethods_1.95.0 +## [89] gtable_0.3.4 sass_0.4.9 +## [91] digest_0.6.35 SparseArray_1.3.5 +## [93] farver_2.1.1 htmlwidgets_1.6.4 +## [95] memoise_2.0.1 htmltools_0.5.8.1 +## [97] pkgdown_2.0.8.9000 lifecycle_1.0.4 +## [99] httr_1.4.7 statmod_1.5.0 +## [101] MASS_7.3-60.2
## R Under development (unstable) (2024-04-10 r86396) ## Platform: x86_64-pc-linux-gnu ## Running under: Ubuntu 22.04.4 LTS ## @@ -2227,65 +2227,67 @@ Session information## ## other attached packages: ## [1] SummarizedExperiment_1.33.3 Biobase_2.63.1 -## [3] GenomicRanges_1.55.4 GenomeInfoDb_1.39.10 -## [5] IRanges_2.37.1 S4Vectors_0.41.5 +## [3] GenomicRanges_1.55.4 GenomeInfoDb_1.39.13 +## [5] IRanges_2.37.1 S4Vectors_0.41.6 ## [7] BiocGenerics_0.49.1 MatrixGenerics_1.15.0 -## [9] matrixStats_1.2.0 MsExperiment_1.5.4 +## [9] matrixStats_1.3.0 MsExperiment_1.5.4 ## [11] ProtGenerics_1.35.4 pheatmap_1.0.12 ## [13] RColorBrewer_1.1-3 pander_0.6.5 -## [15] faahKO_1.43.0 xcms_4.1.12 +## [15] faahKO_1.43.0 xcms_4.1.13 ## [17] BiocParallel_1.37.1 BiocStyle_2.31.0 ## ## loaded via a namespace (and not attached): -## [1] DBI_1.2.2 rlang_1.1.3 -## [3] magrittr_2.0.3 clue_0.3-65 -## [5] MassSpecWavelet_1.69.0 compiler_4.5.0 -## [7] systemfonts_1.0.6 vctrs_0.6.5 -## [9] MetaboCoreUtils_1.11.2 pkgconfig_2.0.3 -## [11] crayon_1.5.2 fastmap_1.1.1 -## [13] XVector_0.43.1 utf8_1.2.4 -## [15] rmarkdown_2.26 preprocessCore_1.65.0 -## [17] ragg_1.3.0 purrr_1.0.2 -## [19] xfun_0.43 MultiAssayExperiment_1.29.1 -## [21] zlibbioc_1.49.3 cachem_1.0.8 -## [23] jsonlite_1.8.8 progress_1.2.3 -## [25] highr_0.10 DelayedArray_0.29.9 -## [27] prettyunits_1.2.0 parallel_4.5.0 -## [29] cluster_2.1.6 R6_2.5.1 -## [31] bslib_0.7.0 limma_3.59.6 -## [33] jquerylib_0.1.4 Rcpp_1.0.12 -## [35] bookdown_0.38 iterators_1.0.14 -## [37] knitr_1.45 Matrix_1.7-0 -## [39] igraph_2.0.3 tidyselect_1.2.1 -## [41] abind_1.4-5 yaml_2.3.8 -## [43] doParallel_1.0.17 codetools_0.2-20 -## [45] affy_1.81.0 lattice_0.22-6 -## [47] tibble_3.2.1 plyr_1.8.9 -## [49] evaluate_0.23 desc_1.4.3 -## [51] Spectra_1.13.8 pillar_1.9.0 -## [53] affyio_1.73.0 BiocManager_1.30.22 -## [55] foreach_1.5.2 MSnbase_2.29.4 -## [57] MALDIquant_1.22.2 ncdf4_1.22 -## [59] generics_0.1.3 hms_1.1.3 -## [61] ggplot2_3.5.0 munsell_0.5.1 -## [63] scales_1.3.0 glue_1.7.0 -## [65] MsFeatures_1.11.0 lazyeval_0.2.2 -## [67] tools_4.5.0 mzID_1.41.0 -## [69] QFeatures_1.13.3 vsn_3.71.1 -## [71] mzR_2.37.3 fs_1.6.3 -## [73] XML_3.99-0.16.1 grid_4.5.0 -## [75] impute_1.77.0 MsCoreUtils_1.15.6 -## [77] colorspace_2.1-0 GenomeInfoDbData_1.2.12 -## [79] PSMatch_1.7.2 cli_3.6.2 -## [81] textshaping_0.3.7 fansi_1.0.6 -## [83] S4Arrays_1.3.6 dplyr_1.1.4 -## [85] AnnotationFilter_1.27.0 pcaMethods_1.95.0 -## [87] gtable_0.3.4 sass_0.4.9 -## [89] digest_0.6.35 SparseArray_1.3.4 -## [91] farver_2.1.1 htmlwidgets_1.6.4 -## [93] memoise_2.0.1 htmltools_0.5.8.1 -## [95] pkgdown_2.0.7.9000 lifecycle_1.0.4 -## [97] statmod_1.5.0 MASS_7.3-60.2
rtimeDifferenceThreshold
ObiwarpParam
LamaParama
adjustRtime()
matchLamasChromPeaks()
summarizeMatchLama()
plot(LamaParama)
filterFeatures,PercentMissingFilter
.empty_chrom_peaks
sn
manualChromPeaks
filterFeatures
filter
RsdFilter
DratioFilter
PercentMissingFilter
BlankFlag
XcmsResult
SummarizedExperiment
filterSpectra
MsExperiment
breaks_ppm
MsCoreUtils
featureArea
featureChromatograms
PeakDensityParam
chromatogram
XcmsExperiment
data
faahko
verboseBetaColumns
CentWaveParam
param =
storeResults
PlainTextParam
RDataParam
The value for the slot.