Site built with pkgdown 2.0.8.9000.
+Site built with pkgdown 2.0.9.9000.
diff --git a/apple-touch-icon-120x120.png b/apple-touch-icon-120x120.png index 9de97c12..8dfd07f2 100644 Binary files a/apple-touch-icon-120x120.png and b/apple-touch-icon-120x120.png differ diff --git a/apple-touch-icon-152x152.png b/apple-touch-icon-152x152.png index 9c0f24ae..513d2b1e 100644 Binary files a/apple-touch-icon-152x152.png and b/apple-touch-icon-152x152.png differ diff --git a/apple-touch-icon-180x180.png b/apple-touch-icon-180x180.png index 296a7eb6..d43a71ae 100644 Binary files a/apple-touch-icon-180x180.png and b/apple-touch-icon-180x180.png differ diff --git a/apple-touch-icon-60x60.png b/apple-touch-icon-60x60.png index 339ccab2..652d86d0 100644 Binary files a/apple-touch-icon-60x60.png and b/apple-touch-icon-60x60.png differ diff --git a/apple-touch-icon-76x76.png b/apple-touch-icon-76x76.png index 3c343459..43e95fa0 100644 Binary files a/apple-touch-icon-76x76.png and b/apple-touch-icon-76x76.png differ diff --git a/apple-touch-icon.png b/apple-touch-icon.png index b04593f2..6e751ee3 100644 Binary files a/apple-touch-icon.png and b/apple-touch-icon.png differ diff --git a/articles/Processing.html b/articles/Processing.html index 98f19f1f..ba7b996c 100644 --- a/articles/Processing.html +++ b/articles/Processing.html @@ -40,7 +40,7 @@ @@ -650,7 +650,7 @@## R Under development (unstable) (2024-04-10 r86396)
+## R version 4.4.0 (2024-04-24)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 22.04.4 LTS
##
@@ -659,12 +659,7 @@ Session information## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so; LAPACK version 3.10.0
##
## locale:
-## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
-## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
-## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
-## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
-## [9] LC_ADDRESS=C LC_TELEPHONE=C
-## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
+## [1] C
##
## time zone: UTC
## tzcode source: system (glibc)
@@ -675,47 +670,48 @@ Session information##
## other attached packages:
## [1] gplots_3.1.3.1 dplyr_1.1.4
-## [3] ggplot2_3.5.0 QFeatures_1.13.7
-## [5] MultiAssayExperiment_1.29.1 SummarizedExperiment_1.33.3
-## [7] Biobase_2.63.1 GenomicRanges_1.55.4
-## [9] GenomeInfoDb_1.39.13 IRanges_2.37.1
-## [11] S4Vectors_0.41.6 BiocGenerics_0.49.1
-## [13] MatrixGenerics_1.15.0 matrixStats_1.3.0
-## [15] BiocStyle_2.31.0
+## [3] ggplot2_3.5.1 QFeatures_1.15.1
+## [5] MultiAssayExperiment_1.31.1 SummarizedExperiment_1.35.0
+## [7] Biobase_2.65.0 GenomicRanges_1.57.0
+## [9] GenomeInfoDb_1.41.0 IRanges_2.39.0
+## [11] S4Vectors_0.43.0 BiocGenerics_0.51.0
+## [13] MatrixGenerics_1.17.0 matrixStats_1.3.0
+## [15] BiocStyle_2.33.0
##
## loaded via a namespace (and not attached):
## [1] tidyselect_1.2.1 farver_2.1.1 bitops_1.0-7
-## [4] fastmap_1.1.1 lazyeval_0.2.2 RCurl_1.98-1.14
-## [7] digest_0.6.35 lifecycle_1.0.4 cluster_2.1.6
-## [10] ProtGenerics_1.35.4 statmod_1.5.0 magrittr_2.0.3
-## [13] compiler_4.5.0 rlang_1.1.3 sass_0.4.9
-## [16] tools_4.5.0 igraph_2.0.3 utf8_1.2.4
-## [19] yaml_2.3.8 knitr_1.46 labeling_0.4.3
-## [22] S4Arrays_1.3.7 htmlwidgets_1.6.4 DelayedArray_0.29.9
-## [25] abind_1.4-5 KernSmooth_2.23-22 withr_3.0.0
-## [28] purrr_1.0.2 desc_1.4.3 grid_4.5.0
+## [4] fastmap_1.1.1 lazyeval_0.2.2 digest_0.6.35
+## [7] lifecycle_1.0.4 cluster_2.1.6 ProtGenerics_1.35.4
+## [10] statmod_1.5.0 magrittr_2.0.3 compiler_4.4.0
+## [13] rlang_1.1.3 sass_0.4.9 tools_4.4.0
+## [16] igraph_2.0.3 utf8_1.2.4 yaml_2.3.8
+## [19] knitr_1.46 labeling_0.4.3 S4Arrays_1.5.0
+## [22] htmlwidgets_1.6.4 DelayedArray_0.31.0 plyr_1.8.9
+## [25] KernSmooth_2.23-22 abind_1.4-5 withr_3.0.0
+## [28] purrr_1.0.2 desc_1.4.3 grid_4.4.0
## [31] fansi_1.0.6 caTools_1.18.2 colorspace_2.1-0
## [34] scales_1.3.0 gtools_3.9.5 MASS_7.3-60.2
-## [37] cli_3.6.2 rmarkdown_2.26 crayon_1.5.2
-## [40] ragg_1.3.0 generics_0.1.3 httr_1.4.7
-## [43] BiocBaseUtils_1.5.1 cachem_1.0.8 zlibbioc_1.49.3
-## [46] AnnotationFilter_1.27.0 BiocManager_1.30.22 XVector_0.43.1
-## [49] vctrs_0.6.5 Matrix_1.7-0 jsonlite_1.8.8
-## [52] bookdown_0.38 clue_0.3-65 systemfonts_1.0.6
-## [55] limma_3.59.8 tidyr_1.3.1 jquerylib_0.1.4
-## [58] glue_1.7.0 pkgdown_2.0.8.9000 gtable_0.3.4
-## [61] UCSC.utils_0.99.5 munsell_0.5.1 tibble_3.2.1
-## [64] pillar_1.9.0 htmltools_0.5.8.1 GenomeInfoDbData_1.2.12
-## [67] R6_2.5.1 textshaping_0.3.7 evaluate_0.23
-## [70] lattice_0.22-6 highr_0.10 msdata_0.43.0
-## [73] memoise_2.0.1 bslib_0.7.0 SparseArray_1.3.5
-## [76] xfun_0.43 MsCoreUtils_1.15.6 fs_1.6.3
-## [79] pkgconfig_2.0.3
+## [37] cli_3.6.2 rmarkdown_2.26.2 crayon_1.5.2
+## [40] ragg_1.3.1 generics_0.1.3 httr_1.4.7
+## [43] reshape2_1.4.4 BiocBaseUtils_1.7.0 cachem_1.0.8
+## [46] stringr_1.5.1 zlibbioc_1.51.0 AnnotationFilter_1.29.0
+## [49] BiocManager_1.30.23 XVector_0.45.0 vctrs_0.6.5
+## [52] Matrix_1.7-0 jsonlite_1.8.8 bookdown_0.39
+## [55] clue_0.3-65 systemfonts_1.0.6 limma_3.61.0
+## [58] jquerylib_0.1.4 tidyr_1.3.1 glue_1.7.0
+## [61] pkgdown_2.0.9.9000 stringi_1.8.4 gtable_0.3.5
+## [64] UCSC.utils_1.1.0 munsell_0.5.1 tibble_3.2.1
+## [67] pillar_1.9.0 htmltools_0.5.8.1 GenomeInfoDbData_1.2.12
+## [70] R6_2.5.1 textshaping_0.3.7 evaluate_0.23
+## [73] lattice_0.22-6 highr_0.10 msdata_0.45.0
+## [76] memoise_2.0.1 bslib_0.7.0 Rcpp_1.0.12
+## [79] SparseArray_1.5.1 xfun_0.43 MsCoreUtils_1.17.0
+## [82] fs_1.6.4 pkgconfig_2.0.3Site built with pkgdown 2.0.8.9000.
+Site built with pkgdown 2.0.9.9000.
QFeatures object## 5 1.70 25.56 Plasma mem...
## 6 -0.67 21.27 Nucleus - ...
For further details on how to manipulate such objects, refer to the -MultiAssayExperiment -(Ramos et al. 2017) and SummerizedExperiment +MultiAssayExperiment +(Ramos et al. 2017) and SummerizedExperiment (Morgan et al. 2019) packages.
As illustrated in figure @ref(fig:featuresplot), an central
characteristic of QFeatures objects is the aggregative
@@ -280,7 +280,7 @@
QFeatures object## dim: 2923 10
## metadata(0):
## assays(2): assay aggcounts
-## rownames(2923): aAADADVSLHNFSAR aAADPSEk ... yYSFFDLNPk YYSIASSSk
+## rownames(2923): AAAVSTEGk AAIDYQk ... ykVEEASDLSISk ykVPQTEEPTAk
## rowData names(7): Sequence ProteinDescriptions ... markers .n
## colnames(10): X126 X127C ... X130N X131
## colData names(0):
@@ -370,11 +370,11 @@ ## R Under development (unstable) (2024-04-10 r86396)
+## R version 4.4.0 (2024-04-24)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 22.04.4 LTS
##
@@ -599,12 +599,7 @@ Session information## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so; LAPACK version 3.10.0
##
## locale:
-## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
-## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
-## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
-## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
-## [9] LC_ADDRESS=C LC_TELEPHONE=C
-## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
+## [1] C
##
## time zone: UTC
## tzcode source: system (glibc)
@@ -614,45 +609,46 @@ Session information## [8] base
##
## other attached packages:
-## [1] ggplot2_3.5.0 QFeatures_1.13.7
-## [3] MultiAssayExperiment_1.29.1 SummarizedExperiment_1.33.3
-## [5] Biobase_2.63.1 GenomicRanges_1.55.4
-## [7] GenomeInfoDb_1.39.13 IRanges_2.37.1
-## [9] S4Vectors_0.41.6 BiocGenerics_0.49.1
-## [11] MatrixGenerics_1.15.0 matrixStats_1.3.0
-## [13] BiocStyle_2.31.0
+## [1] ggplot2_3.5.1 QFeatures_1.15.1
+## [3] MultiAssayExperiment_1.31.1 SummarizedExperiment_1.35.0
+## [5] Biobase_2.65.0 GenomicRanges_1.57.0
+## [7] GenomeInfoDb_1.41.0 IRanges_2.39.0
+## [9] S4Vectors_0.43.0 BiocGenerics_0.51.0
+## [11] MatrixGenerics_1.17.0 matrixStats_1.3.0
+## [13] BiocStyle_2.33.0
##
## loaded via a namespace (and not attached):
-## [1] gtable_0.3.4 xfun_0.43 bslib_0.7.0
+## [1] gtable_0.3.5 xfun_0.43 bslib_0.7.0
## [4] htmlwidgets_1.6.4 lattice_0.22-6 generics_0.1.3
-## [7] vctrs_0.6.5 tools_4.5.0 bitops_1.0-7
-## [10] tibble_3.2.1 fansi_1.0.6 highr_0.10
-## [13] cluster_2.1.6 BiocBaseUtils_1.5.1 pkgconfig_2.0.3
-## [16] Matrix_1.7-0 desc_1.4.3 lifecycle_1.0.4
-## [19] GenomeInfoDbData_1.2.12 farver_2.1.1 compiler_4.5.0
+## [7] vctrs_0.6.5 tools_4.4.0 tibble_3.2.1
+## [10] fansi_1.0.6 highr_0.10 cluster_2.1.6
+## [13] BiocBaseUtils_1.7.0 pkgconfig_2.0.3 Matrix_1.7-0
+## [16] desc_1.4.3 lifecycle_1.0.4 GenomeInfoDbData_1.2.12
+## [19] farver_2.1.1 compiler_4.4.0 stringr_1.5.1
## [22] textshaping_0.3.7 munsell_0.5.1 clue_0.3-65
-## [25] htmltools_0.5.8.1 sass_0.4.9 RCurl_1.98-1.14
-## [28] yaml_2.3.8 lazyeval_0.2.2 pillar_1.9.0
-## [31] pkgdown_2.0.8.9000 crayon_1.5.2 jquerylib_0.1.4
-## [34] tidyr_1.3.1 MASS_7.3-60.2 DelayedArray_0.29.9
-## [37] cachem_1.0.8 abind_1.4-5 tidyselect_1.2.1
-## [40] digest_0.6.35 dplyr_1.1.4 purrr_1.0.2
-## [43] bookdown_0.38 labeling_0.4.3 fastmap_1.1.1
-## [46] grid_4.5.0 colorspace_2.1-0 cli_3.6.2
-## [49] SparseArray_1.3.5 magrittr_2.0.3 S4Arrays_1.3.7
-## [52] utf8_1.2.4 withr_3.0.0 scales_1.3.0
-## [55] UCSC.utils_0.99.5 rmarkdown_2.26 XVector_0.43.1
-## [58] httr_1.4.7 igraph_2.0.3 ragg_1.3.0
-## [61] memoise_2.0.1 evaluate_0.23 knitr_1.46
-## [64] rlang_1.1.3 glue_1.7.0 BiocManager_1.30.22
-## [67] jsonlite_1.8.8 AnnotationFilter_1.27.0 R6_2.5.1
-## [70] systemfonts_1.0.6 fs_1.6.3 zlibbioc_1.49.3
-## [73] ProtGenerics_1.35.4 MsCoreUtils_1.15.6
+## [25] htmltools_0.5.8.1 sass_0.4.9 yaml_2.3.8
+## [28] lazyeval_0.2.2 pillar_1.9.0 tidyr_1.3.1
+## [31] pkgdown_2.0.9.9000 crayon_1.5.2 jquerylib_0.1.4
+## [34] MASS_7.3-60.2 DelayedArray_0.31.0 cachem_1.0.8
+## [37] abind_1.4-5 tidyselect_1.2.1 digest_0.6.35
+## [40] stringi_1.8.4 dplyr_1.1.4 reshape2_1.4.4
+## [43] purrr_1.0.2 bookdown_0.39 labeling_0.4.3
+## [46] fastmap_1.1.1 grid_4.4.0 colorspace_2.1-0
+## [49] cli_3.6.2 SparseArray_1.5.1 magrittr_2.0.3
+## [52] S4Arrays_1.5.0 utf8_1.2.4 withr_3.0.0
+## [55] scales_1.3.0 UCSC.utils_1.1.0 rmarkdown_2.26.2
+## [58] XVector_0.45.0 httr_1.4.7 igraph_2.0.3
+## [61] ragg_1.3.1 memoise_2.0.1 evaluate_0.23
+## [64] knitr_1.46 rlang_1.1.3 Rcpp_1.0.12
+## [67] glue_1.7.0 BiocManager_1.30.23 jsonlite_1.8.8
+## [70] AnnotationFilter_1.29.0 R6_2.5.1 plyr_1.8.9
+## [73] systemfonts_1.0.6 fs_1.6.4 zlibbioc_1.51.0
+## [76] ProtGenerics_1.35.4 MsCoreUtils_1.17.0Site built with pkgdown 2.0.8.9000.
+Site built with pkgdown 2.0.9.9000.
## R Under development (unstable) (2024-04-10 r86396)
+## R version 4.4.0 (2024-04-24)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 22.04.4 LTS
##
@@ -330,12 +330,7 @@ Session information## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so; LAPACK version 3.10.0
##
## locale:
-## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
-## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
-## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
-## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
-## [9] LC_ADDRESS=C LC_TELEPHONE=C
-## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
+## [1] C
##
## time zone: UTC
## tzcode source: system (glibc)
@@ -345,49 +340,50 @@ Session information## [8] methods base
##
## other attached packages:
-## [1] ComplexHeatmap_2.19.0 ggplot2_3.5.0
-## [3] QFeatures_1.13.7 MultiAssayExperiment_1.29.1
-## [5] SummarizedExperiment_1.33.3 Biobase_2.63.1
-## [7] GenomicRanges_1.55.4 GenomeInfoDb_1.39.13
-## [9] IRanges_2.37.1 S4Vectors_0.41.6
-## [11] BiocGenerics_0.49.1 MatrixGenerics_1.15.0
-## [13] matrixStats_1.3.0 BiocStyle_2.31.0
+## [1] ComplexHeatmap_2.21.0 ggplot2_3.5.1
+## [3] QFeatures_1.15.1 MultiAssayExperiment_1.31.1
+## [5] SummarizedExperiment_1.35.0 Biobase_2.65.0
+## [7] GenomicRanges_1.57.0 GenomeInfoDb_1.41.0
+## [9] IRanges_2.39.0 S4Vectors_0.43.0
+## [11] BiocGenerics_0.51.0 MatrixGenerics_1.17.0
+## [13] matrixStats_1.3.0 BiocStyle_2.33.0
##
## loaded via a namespace (and not attached):
## [1] tidyselect_1.2.1 dplyr_1.1.4 farver_2.1.1
-## [4] bitops_1.0-7 fastmap_1.1.1 lazyeval_0.2.2
-## [7] RCurl_1.98-1.14 digest_0.6.35 lifecycle_1.0.4
-## [10] cluster_2.1.6 ProtGenerics_1.35.4 magrittr_2.0.3
-## [13] compiler_4.5.0 rlang_1.1.3 sass_0.4.9
-## [16] tools_4.5.0 igraph_2.0.3 utf8_1.2.4
-## [19] yaml_2.3.8 knitr_1.46 S4Arrays_1.3.7
-## [22] labeling_0.4.3 htmlwidgets_1.6.4 DelayedArray_0.29.9
-## [25] RColorBrewer_1.1-3 abind_1.4-5 withr_3.0.0
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-## [43] cachem_1.0.8 zlibbioc_1.49.3 parallel_4.5.0
-## [46] AnnotationFilter_1.27.0 BiocManager_1.30.22 XVector_0.43.1
-## [49] vctrs_0.6.5 Matrix_1.7-0 jsonlite_1.8.8
-## [52] bookdown_0.38 GetoptLong_1.0.5 clue_0.3-65
-## [55] magick_2.8.3 systemfonts_1.0.6 foreach_1.5.2
-## [58] tidyr_1.3.1 jquerylib_0.1.4 glue_1.7.0
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-## [82] SparseArray_1.3.5 xfun_0.43 GlobalOptions_0.1.2
-## [85] MsCoreUtils_1.15.6 fs_1.6.3 pkgconfig_2.0.3
+## [4] fastmap_1.1.1 lazyeval_0.2.2 digest_0.6.35
+## [7] lifecycle_1.0.4 cluster_2.1.6 ProtGenerics_1.35.4
+## [10] magrittr_2.0.3 compiler_4.4.0 rlang_1.1.3
+## [13] sass_0.4.9 tools_4.4.0 igraph_2.0.3
+## [16] utf8_1.2.4 yaml_2.3.8 knitr_1.46
+## [19] S4Arrays_1.5.0 labeling_0.4.3 htmlwidgets_1.6.4
+## [22] DelayedArray_0.31.0 RColorBrewer_1.1-3 plyr_1.8.9
+## [25] abind_1.4-5 withr_3.0.0 purrr_1.0.2
+## [28] desc_1.4.3 fansi_1.0.6 colorspace_2.1-0
+## [31] iterators_1.0.14 scales_1.3.0 MASS_7.3-60.2
+## [34] cli_3.6.2 rmarkdown_2.26.2 crayon_1.5.2
+## [37] ragg_1.3.1 generics_0.1.3 rjson_0.2.21
+## [40] httr_1.4.7 reshape2_1.4.4 BiocBaseUtils_1.7.0
+## [43] cachem_1.0.8 stringr_1.5.1 zlibbioc_1.51.0
+## [46] parallel_4.4.0 AnnotationFilter_1.29.0 BiocManager_1.30.23
+## [49] XVector_0.45.0 vctrs_0.6.5 Matrix_1.7-0
+## [52] jsonlite_1.8.8 bookdown_0.39 GetoptLong_1.0.5
+## [55] clue_0.3-65 magick_2.8.3 systemfonts_1.0.6
+## [58] foreach_1.5.2 jquerylib_0.1.4 tidyr_1.3.1
+## [61] glue_1.7.0 pkgdown_2.0.9.9000 codetools_0.2-20
+## [64] shape_1.4.6.1 stringi_1.8.4 gtable_0.3.5
+## [67] UCSC.utils_1.1.0 munsell_0.5.1 tibble_3.2.1
+## [70] pillar_1.9.0 htmltools_0.5.8.1 circlize_0.4.16
+## [73] GenomeInfoDbData_1.2.12 R6_2.5.1 textshaping_0.3.7
+## [76] doParallel_1.0.17 evaluate_0.23 lattice_0.22-6
+## [79] highr_0.10 png_0.1-8 memoise_2.0.1
+## [82] bslib_0.7.0 Rcpp_1.0.12 SparseArray_1.5.1
+## [85] xfun_0.43 GlobalOptions_0.1.2 MsCoreUtils_1.17.0
+## [88] fs_1.6.4 pkgconfig_2.0.3Site built with pkgdown 2.0.8.9000.
+Site built with pkgdown 2.0.9.9000.
Gatto L, Vanderaa C (2024). QFeatures: Quantitative features for mass spectrometry data. -R package version 1.13.7, https://github.com/RforMassSpectrometry/QFeatures. +R package version 1.15.1, https://github.com/RforMassSpectrometry/QFeatures.
@Manual{,
title = {QFeatures: Quantitative features for mass spectrometry data},
author = {Laurent Gatto and Christophe Vanderaa},
year = {2024},
- note = {R package version 1.13.7},
+ note = {R package version 1.15.1},
url = {https://github.com/RforMassSpectrometry/QFeatures},
}
@@ -104,7 +104,7 @@ NEWS.md
+ reshape2::melt, required for MultiAssayExperiment::longFormat().# S4 method for AssayLink
+ # S4 method for class 'AssayLink'
show(object)
-# S4 method for AssayLinks
+# S4 method for class 'AssayLinks'
updateObject(object, ..., verbose = FALSE)
-# S4 method for AssayLink
+# S4 method for class 'AssayLink'
updateObject(object, ..., verbose = FALSE)
AssayLink(name, from = NA_character_, fcol = NA_character_, hits = Hits())
@@ -90,10 +90,10 @@ Links between Assays
assayLinks(x, i)
-# S4 method for AssayLink,character,ANY,ANY
+# S4 method for class 'AssayLink,character,ANY,ANY'
[(x, i, j, ..., drop = TRUE)
-# S4 method for AssayLinks,list,ANY,ANY
+# S4 method for class 'AssayLinks,list,ANY,ANY'
[(x, i, j, ..., drop = TRUE)
addAssayLink(object, from, to, varFrom, varTo)
@@ -103,76 +103,76 @@ Links between Assays
Arguments
- - object
+ - object
An AssayLink object to show.
- ...
+- ...
A set of AssayLink objects or a list thereof.
- verbose
+- verbose
logical (default FALSE) whether to print extra messages
- name
+- name
A mandatory name of the assay(s).
- from
+- from
A character() or integer() indicating which
assay(s) to link from in object
- fcol
+- fcol
The feature variable of the parent assay used to
generate the current assay (used in
aggregateFeatures). NA_character_, if not applicable.
- hits
+- hits
An object of class S4Vectors::Hits matching the
features of two assays.
- names
+- names
A character() of AssayLink names. If provided,
... are ignored, and names is used to create an
AssayLinks object with AssayLink instances with names
names.
- x
+- x
An instance of class QFeatures.
- i
+- i
The index or name of the assay whose AssayLink and
parents AssayLink instances are to be returned. For [, the
feature names to filter on.
- j
+- j
ignored.
- drop
+- drop
ignored.
- to
+- to
A character(1) or integer(1) indicating which assay
to link to in object
- varFrom
+- varFrom
A character() indicating the feature variable(s)
to use to match the from assay(s) to the to
assay. varFrom must have the same length as from and is
assumed to be ordered as from.
- varTo
+- varTo
A character(1) indicating the feature variable to
use to match the to assay to the from assay(s).
Examples
diff --git a/reference/QFeatures-aggregate.html b/reference/QFeatures-aggregate.html
index ae65e1cd..d75409fa 100644
--- a/reference/QFeatures-aggregate.html
+++ b/reference/QFeatures-aggregate.html
@@ -30,7 +30,7 @@
# S4 method for QFeatures
+ # S4 method for class 'QFeatures'
aggregateFeatures(
object,
i,
@@ -105,60 +105,60 @@ Aggregate an assay's quantitative features
...
)
-# S4 method for SummarizedExperiment
+# S4 method for class 'SummarizedExperiment'
aggregateFeatures(object, fcol, fun = MsCoreUtils::robustSummary, ...)
-# S4 method for QFeatures
+# S4 method for class 'QFeatures'
adjacencyMatrix(object, i, adjName = "adjacencyMatrix")
adjacencyMatrix(object, i, adjName = "adjacencyMatrix") <- value
-# S4 method for SummarizedExperiment
+# S4 method for class 'SummarizedExperiment'
aggcounts(object, ...)
An instance of class SummarizedExperiment or
QFeatures.
When adding an adjacency matrix to an assay of a
QFeatures object, the index or name of the assay the
adjacency matrix will be added to. Ignored when x is an
SummarizedExperiment.
A character(1) naming a rowdata variable (of assay
i in case of a QFeatures) defining how to aggregate the
features of the assay. This variable is either a character
or a (possibly sparse) matrix. See below for details.
A character(1) naming the new assay. Default is
newAssay. Note that the function will fail if there's
already an assay with name.
A function used for quantitative feature aggregation. See Details for examples.
Additional parameters passed the fun.
character(1) with the variable name containing
the adjacency matrix. Default is "adjacencyMatrix".
An adjacency matrix with row and column names. The
matrix will be coerced to compressed, column-oriented sparse
matrix (class dgCMatrix) as defined in the Matrix package,
@@ -502,7 +502,7 @@
QFeatures(..., assayLinks = NULL)
-# S4 method for QFeatures
+# S4 method for class 'QFeatures'
show(object)
-# S3 method for QFeatures
+# S3 method for class 'QFeatures'
plot(x, interactive = FALSE, ...)
-# S4 method for QFeatures,ANY,ANY,ANY
+# S4 method for class 'QFeatures,ANY,ANY,ANY'
[(x, i, j, ..., drop = TRUE)
-# S4 method for QFeatures,character,ANY,ANY
+# S4 method for class 'QFeatures,character,ANY,ANY'
[(x, i, j, k, ..., drop = TRUE)
-# S4 method for QFeatures
+# S4 method for class 'QFeatures'
c(x, ...)
-# S4 method for QFeatures
+# S4 method for class 'QFeatures'
dims(x, use.names = TRUE)
-# S4 method for QFeatures
+# S4 method for class 'QFeatures'
nrows(x, use.names = TRUE)
-# S4 method for QFeatures
+# S4 method for class 'QFeatures'
ncols(x, use.names = TRUE)
-# S4 method for QFeatures
+# S4 method for class 'QFeatures'
rowData(x, use.names = TRUE, ...)
-# S4 method for QFeatures,DataFrameList
+# S4 method for class 'QFeatures,DataFrameList'
rowData(x) <- value
-# S4 method for QFeatures,ANY
+# S4 method for class 'QFeatures,ANY'
rowData(x) <- value
rbindRowData(object, i)
@@ -158,7 +158,7 @@ Quantitative MS QFeatures
rowDataNames(x)
-# S4 method for QFeatures,character
+# S4 method for class 'QFeatures,character'
names(x) <- value
longFormat(object, colvars = NULL, rowvars = NULL, index = 1L)
@@ -169,10 +169,10 @@ Quantitative MS QFeatures
replaceAssay(x, y, i)
-# S4 method for QFeatures,ANY,ANY
+# S4 method for class 'QFeatures,ANY,ANY'
[[(x, i, j, ...) <- value
-# S4 method for QFeatures
+# S4 method for class 'QFeatures'
updateObject(object, ..., verbose = FALSE)
dropEmptyAssays(object, dims = 1:2)See MultiAssayExperiment for details. For plot,
further arguments passed to igraph::plot.igraph.
An optional AssayLinks.
An instance of class QFeatures.
An instance of class QFeatures.
A logical(1). If TRUE, an interactive graph
is generated using plotly. Else, a static plot using igraph
is generated. We recommend interactive exploration when the
QFeatures object contains more than 50 assays.
An indexing vector. See the corresponding section in the documentation for more details.
character(), logical(), or numeric() vector for
subsetting by colData rows.
logical (default TRUE) whether to drop empty assay
elements in the ExperimentList.
character(), logical(), or numeric() vector for
subsetting by assays
A logical(1) indicating whether the rownames of
each assay should be propagated to the corresponding rowData.
The values to use as a replacement. See the corresponding section in the documentation for more details.
A character() with the names of the rowData
variables (columns) to retain in any assay.
A character() that selects column(s) in the
colData.
The assay indicator within each SummarizedExperiment
object. A vector input is supported in the case that the
SummarizedExperiment object(s) has more than one assay
(default 1L)
An object that inherits from SummarizedExperiment or a
named list of assays. When y is a list, each element must
inherit from a SummarizedExperiment and the names of the
@@ -260,16 +260,16 @@
x.A character(1) naming the single assay. Ignored if
y is a list of assays.
logical (default FALSE) whether to print extra messages
numeric() that defines the dimensions to consider to
drop empty assays. 1 for rows (i.e. assays without any
features) and 2 for columns (i.e. assays without any
@@ -508,7 +508,7 @@
VariableFilter(field, value, condition = "==", not = FALSE)
-# S4 method for QFeatures,AnnotationFilter
+# S4 method for class 'QFeatures,AnnotationFilter'
filterFeatures(object, filter, i, na.rm = FALSE, keep = FALSE, ...)
-# S4 method for QFeatures,formula
+# S4 method for class 'QFeatures,formula'
filterFeatures(object, filter, i, na.rm = FALSE, keep = FALSE, ...)character(1) refering to the name of the variable
to apply the filter on.
character() or integer() value for the
CharacterVariableFilter and NumericVariableFilter filters
respectively.
character(1) defining the condition to be used in
the filter. For NumericVariableFilter, one of "==",
"!=", ">", "<", ">=" or "<=". For
@@ -108,39 +108,39 @@
"==".logical(1) indicating whether the filtering should be negated
or not. TRUE indicates is negated (!). FALSE indicates not negated.
Default not is FALSE, so no negation.
An instance of class QFeatures.
Either an instance of class AnnotationFilter or a formula.
A numeric, logical or character vector pointing to the assay(s) to be filtered.
logical(1) indicating whether missing values should
be removed. Default is FALSE.
logical(1) indicating whether to keep the features
of assays for which at least one of the filtering variables are
missing in the rowData. When FALSE (default), all such assay
will contain 0 features; when TRUE, the assays are untouched.
Additional parameters. Currently ignored.
# S4 method for SummarizedExperiment,missing
+ # S4 method for class 'SummarizedExperiment,missing'
zeroIsNA(object, i)
-# S4 method for QFeatures,integer
+# S4 method for class 'QFeatures,integer'
zeroIsNA(object, i)
-# S4 method for QFeatures,numeric
+# S4 method for class 'QFeatures,numeric'
zeroIsNA(object, i)
-# S4 method for QFeatures,character
+# S4 method for class 'QFeatures,character'
zeroIsNA(object, i)
-# S4 method for SummarizedExperiment,missing
+# S4 method for class 'SummarizedExperiment,missing'
infIsNA(object, i)
-# S4 method for QFeatures,integer
+# S4 method for class 'QFeatures,integer'
infIsNA(object, i)
-# S4 method for QFeatures,numeric
+# S4 method for class 'QFeatures,numeric'
infIsNA(object, i)
-# S4 method for QFeatures,character
+# S4 method for class 'QFeatures,character'
infIsNA(object, i)
-# S4 method for SummarizedExperiment,missing
+# S4 method for class 'SummarizedExperiment,missing'
nNA(object, i)
-# S4 method for QFeatures,integer
+# S4 method for class 'QFeatures,integer'
nNA(object, i)
-# S4 method for QFeatures,numeric
+# S4 method for class 'QFeatures,numeric'
nNA(object, i)
-# S4 method for QFeatures,character
+# S4 method for class 'QFeatures,character'
nNA(object, i)
-# S4 method for SummarizedExperiment
+# S4 method for class 'SummarizedExperiment'
filterNA(object, pNA = 0)
-# S4 method for QFeatures
+# S4 method for class 'QFeatures'
filterNA(object, pNA = 0, i)
An object of class QFeatures or SummarizedExperiment.
One or more indices or names of the assay(s) to be processed.
numeric(1) providing the maximum proportion of
missing values per feature (row) that is acceptable. Feature
with higher proportions are removed. If 0 (default), features
@@ -257,7 +257,7 @@
# S4 method for SummarizedExperiment
+ # S4 method for class 'SummarizedExperiment'
logTransform(object, base = 2, pc = 0)
-# S4 method for QFeatures
+# S4 method for class 'QFeatures'
logTransform(object, i, name = "logAssay", base = 2, pc = 0)
-# S4 method for SummarizedExperiment
+# S4 method for class 'SummarizedExperiment'
scaleTransform(object, center = TRUE, scale = TRUE)
-# S4 method for QFeatures
+# S4 method for class 'QFeatures'
scaleTransform(object, i, name = "scaledAssay", center = TRUE, scale = TRUE)
-# S4 method for SummarizedExperiment
+# S4 method for class 'SummarizedExperiment'
normalize(object, method, ...)
-# S4 method for QFeatures
+# S4 method for class 'QFeatures'
normalize(object, i, name = "normAssay", method, ...)
-# S4 method for SummarizedExperiment
+# S4 method for class 'SummarizedExperiment'
sweep(x, MARGIN, STATS, FUN = "-", check.margin = TRUE, ...)
-# S4 method for QFeatures
+# S4 method for class 'QFeatures'
sweep(
x,
MARGIN,
@@ -138,74 +138,74 @@ QFeatures processing
Arguments
- - object
+ - object
An object of class QFeatures or SummarizedExperiment.
- base
+- base
numeric(1) providing the base with respect to which
logarithms are computed. Defaults is 2.
- pc
+- pc
numeric(1) with a pseudocount to add to the
quantitative data. Useful when (true) 0 are present in the
data. Default is 0 (no effect).
- i
+- i
A numeric vector or a character vector giving the index or the
name, respectively, of the assay(s) to be processed.
- name
+- name
A character(1) naming the new assay name. Defaults
are logAssay for logTransform, scaledAssay for
scaleTranform and normAssay for normalize.
- center
+- center
logical(1) (default is TRUE) value or
numeric-alike vector of length equal to the number of columns
of object. See base::scale() for details.
- scale
+- scale
logical(1) (default is TRUE) or a numeric-alike
vector of length equal to the number of columns of
object. See base::scale() for details.
- method
+- method
character(1) defining the normalisation method to
apply. See Details.
- ...
+- ...
Additional parameters passed to inner functions.
- x
+- x
An object of class QFeatures or SummarizedExperiment
in sweep.
- MARGIN
+- MARGIN
As in base::sweep(), a vector of indices giving the
extent(s) of x which correspond to STATS.
- STATS
+- STATS
As in base::sweep(), the summary statistic which is
to be swept out.
- FUN
+- FUN
As in base::sweep(), the function to be used to carry
out the sweep.
- check.margin
+- check.margin
As in base::sweep(), a logical. If TRUE
(the default), warn if the length or dimensions of STATS do
not match the specified dimensions of x. Set to FALSE for
@@ -267,7 +267,7 @@
Examples
diff --git a/reference/QFeatures-subsetBy.html b/reference/QFeatures-subsetBy.html
index 57ffdd9b..2f2f8aa5 100644
--- a/reference/QFeatures-subsetBy.html
+++ b/reference/QFeatures-subsetBy.html
@@ -25,7 +25,7 @@
An instance of class QFeatures.
A character of feature names present in an assay in x.
Additional parameters. Ignored.
An object of class QFeatures.
A numeric() or character() vector indicating from
which assays the rowData should be taken.
A character(1) indicating the variable name in
the rowData that contains the grouping variable, for
instance to count the unique number of peptides or proteins
@@ -97,7 +97,7 @@
A character(1) giving the name of the new
variable in the colData where the number of unique features
will be stored. The name cannot already exist in the
@@ -142,7 +142,7 @@
An instance inheriting from MultiAssayExperiment.
A numeric(1) indicating the maximum number of features
(rows) to consider before disabling row clustering and
displaying feature names for speed purposes. Default is 100.
Additional parameters (other than Rowv and labRow,
which are set internally based on the value of n) passed to
heatmap.
impute
-# S4 method for SummarizedExperiment
+# S4 method for class 'SummarizedExperiment'
impute(object, method, ...)
-# S4 method for QFeatures
+# S4 method for class 'QFeatures'
impute(object, method, ..., i, name = "imputedAssay")A SummarizedExperiment or QFeatures object with
missing values to be imputed.
character(1) defining the imputation method. See
imputeMethods() for available ones. See
MsCoreUtils::impute_matrix() for details.
Additional parameters passed to the inner imputation
function. See MsCoreUtils::impute_matrix() for details.
A logical(1) or a character(1) that defines which
element of the QFeatures instance to impute. It cannot be
missing and must be of length one.
A character(1) naming the new assay name. Default
is imputedAssay.
An instance of class QFeatures.
The indices or names of al least two assays to be joined.
A character(1) naming the new assay. Default is
joinedAssay. Note that the function will fail if there's
already an assay with name.
A data.frame, or any object that can be coerced
into a data.frame, holding the quantitative assay. For
readSummarizedExperiment(), this can also be a
@@ -128,39 +128,39 @@
A numeric(), logical() or character()
defining the columns of the assayData that contain the
quantitative data. This information can also be defined in
colData (see details).
For the single- and multi-set cases, an optional
character(1) or numeric(1) indicating the column to be
used as feature names. Note that rownames must be unique
within QFeatures sets.
Same as quantCols. Available for backwards
compatibility. Default is NULL. If both ecol and colData
are set, an error is thrown.
Further arguments that can be passed on to read.csv()
except stringsAsFactors, which is always FALSE. Only
applicable to readSummarizedExperiment().
A data.frame (or any object that can be coerced
to a data.frame) containing sample/column annotations,
including quantCols and runCol (see details).
For the multi-set case, a numeric(1) or
character(1) pointing to the column of assayData (and
colData, is set) that contains the runs/batches. Make sure
@@ -170,17 +170,17 @@
make.namesFor the single-set case, an optional character(1) to
name the set in the QFeatures object. Default is quants.
A logical(1). If TRUE, quantitative
columns that contain only missing values are removed.
A logical(1) indicating whether the progress of
the data reading and formatting should be printed to the
console. Default is TRUE.
A data.frame, or any object that can be coerced
into a data.frame, holding the quantitative assay. For
readSummarizedExperiment(), this can also be a
@@ -101,20 +101,20 @@
A data.frame (or any object that can be coerced
to a data.frame) containing sample/column annotations,
including quantCols and runCol (see details).
A numeric(), logical() or character()
defining the columns of the assayData that contain the
quantitative data. This information can also be defined in
colData (see details).
For the multi-set case, a numeric(1) or
character(1) pointing to the column of assayData (and
colData, is set) that contains the runs/batches. Make sure
@@ -124,14 +124,14 @@
make.namesA character(1) indicating the type of
multiplexing used in the experiment. One of "none" (default,
for label-free experiments) or "mTRAQ" (for plexDIA
experiments).
A data.frame or any object that can be
coerced to a data.frame that contains the data from the
*_ms1_extracted.tsv file generated by DIA-NN. This argument
@@ -140,19 +140,19 @@
plexdia module (see references).Same as quantCols. Available for backwards
compatibility. Default is NULL. If both ecol and colData
are set, an error is thrown.
A logical(1) indicating whether the progress of
the data reading and formatting should be printed to the
console. Default is TRUE.
Further arguments passed to readQFeatures().
DataFrameThe DataFrame to be reduced or expanded.
A ‘vector’ of length nrow(x) defining the grouping
based on which the DataFrame will be shrunk.
logical(1) specifying of an additional column
(called by default .n) with the tally of rows shrunk into on
new row should be added. Note that if already existing, .n
will be silently overwritten.
A logical(1) defining if invariant columns
should be converted to simple lists. Default is TRUE.
A logical(1) specifying whether the non-invariant
columns should be dropped altogether. Default is FALSE.
A DataFrame or data.frame to be unfolded.
character(1) referring to a character variable in x,
that will be used to unfold x.
character(1) passed to strsplit() to split
x[[k]].