diff --git a/404.html b/404.html index bdf96f16..d41a3f75 100644 --- a/404.html +++ b/404.html @@ -39,7 +39,7 @@ QFeatures - 1.15.1 + 1.15.2 diff --git a/NOTES.html b/NOTES.html index 6317cc72..fc8fde5f 100644 --- a/NOTES.html +++ b/NOTES.html @@ -17,7 +17,7 @@ QFeatures - 1.15.1 + 1.15.2 diff --git a/apple-touch-icon-120x120.png b/apple-touch-icon-120x120.png index 8dfd07f2..e6163fdf 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 513d2b1e..f025ec7d 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 d43a71ae..04a2c6d1 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 652d86d0..b44ba855 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 43e95fa0..6af0b639 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 6e751ee3..d79ee598 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 ba7b996c..7c39b128 100644 --- a/articles/Processing.html +++ b/articles/Processing.html @@ -40,7 +40,7 @@ QFeatures - 1.15.1 + 1.15.2 @@ -659,7 +659,12 @@

Session information## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so; LAPACK version 3.10.0 ## ## locale: -## [1] C +## [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 ## ## time zone: UTC ## tzcode source: system (glibc) @@ -670,7 +675,7 @@

Session information## ## other attached packages: ## [1] gplots_3.1.3.1 dplyr_1.1.4 -## [3] ggplot2_3.5.1 QFeatures_1.15.1 +## [3] ggplot2_3.5.1 QFeatures_1.15.2 ## [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 @@ -686,7 +691,7 @@

Session information## [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 +## [22] htmlwidgets_1.6.4 DelayedArray_0.31.1 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 @@ -705,7 +710,7 @@

Session information## [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 +## [79] SparseArray_1.5.3 xfun_0.43 MsCoreUtils_1.17.0 ## [82] fs_1.6.4 pkgconfig_2.0.3
diff --git a/articles/QFeatures.html b/articles/QFeatures.html index 348c9a29..befa1cc8 100644 --- a/articles/QFeatures.html +++ b/articles/QFeatures.html @@ -40,7 +40,7 @@ QFeatures - 1.15.1 + 1.15.2
@@ -280,7 +280,7 @@

Creating QFeatures object## dim: 2923 10 ## metadata(0): ## assays(2): assay aggcounts -## rownames(2923): AAAVSTEGk AAIDYQk ... ykVEEASDLSISk ykVPQTEEPTAk +## rownames(2923): aAADADVSLHNFSAR aAADPSEk ... yYSFFDLNPk YYSIASSSk ## rowData names(7): Sequence ProteinDescriptions ... markers .n ## colnames(10): X126 X127C ... X130N X131 ## colData names(0): @@ -370,11 +370,11 @@

Manipulating feature metadata## DataFrame with 4519 rows and 5 columns ## assay rowname ProteinGroupAccessions markers .n ## <character> <character> <character> <character> <integer> -## 1 peptides AAAVSTEGk Q9ERE8 unknown 1 -## 2 peptides AAIDYQk Q3THS6 unknown 1 -## 3 peptides AAISQPGISE... Q8BP40 Mitochondr... 1 -## 4 peptides AALAHSEIAT... Q9QXS1-3 unknown 1 -## 5 peptides AAMIVNQLSk Q02257 Plasma mem... 1 +## 1 peptides aAADADVSLH... P0C7N9 unknown 1 +## 2 peptides aAADPSEk Q6P9Q6 unknown 1 +## 3 peptides aAAQFLTSTW... Q9D7Z3 Nucleus - ... 1 +## 4 peptides aAASGAAGDk... A2AGT5 unknown 1 +## 5 peptides AAAVSTEGk Q9ERE8 unknown 1 ## ... ... ... ... ... ... ## 4515 proteins Q9Z2V5 Q9Z2V5 unknown 1 ## 4516 proteins Q9Z2W0 Q9Z2W0 unknown 1 @@ -599,7 +599,12 @@

Session information## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so; LAPACK version 3.10.0 ## ## locale: -## [1] C +## [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 ## ## time zone: UTC ## tzcode source: system (glibc) @@ -609,7 +614,7 @@

Session information## [8] base ## ## other attached packages: -## [1] ggplot2_3.5.1 QFeatures_1.15.1 +## [1] ggplot2_3.5.1 QFeatures_1.15.2 ## [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 @@ -629,12 +634,12 @@

Session information## [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 +## [34] MASS_7.3-60.2 DelayedArray_0.31.1 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 +## [49] cli_3.6.2 SparseArray_1.5.3 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 diff --git a/articles/QFeatures_files/figure-html/plotstat-1.png b/articles/QFeatures_files/figure-html/plotstat-1.png index 4898c63d..da39f184 100644 Binary files a/articles/QFeatures_files/figure-html/plotstat-1.png and b/articles/QFeatures_files/figure-html/plotstat-1.png differ diff --git a/articles/QFeatures_files/figure-html/plotstat3-1.png b/articles/QFeatures_files/figure-html/plotstat3-1.png index 1da2aad4..0c272e27 100644 Binary files a/articles/QFeatures_files/figure-html/plotstat3-1.png and b/articles/QFeatures_files/figure-html/plotstat3-1.png differ diff --git a/articles/Visualization.html b/articles/Visualization.html index 4689df41..955d4a8b 100644 --- a/articles/Visualization.html +++ b/articles/Visualization.html @@ -40,7 +40,7 @@ QFeatures - 1.15.1 + 1.15.2 @@ -330,7 +330,12 @@

Session information## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so; LAPACK version 3.10.0 ## ## locale: -## [1] C +## [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 ## ## time zone: UTC ## tzcode source: system (glibc) @@ -341,7 +346,7 @@

Session information## ## other attached packages: ## [1] ComplexHeatmap_2.21.0 ggplot2_3.5.1 -## [3] QFeatures_1.15.1 MultiAssayExperiment_1.31.1 +## [3] QFeatures_1.15.2 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 @@ -356,7 +361,7 @@

Session information## [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 +## [22] DelayedArray_0.31.1 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 @@ -376,7 +381,7 @@

Session information## [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 +## [82] bslib_0.7.0 Rcpp_1.0.12 SparseArray_1.5.3 ## [85] xfun_0.43 GlobalOptions_0.1.2 MsCoreUtils_1.17.0 ## [88] fs_1.6.4 pkgconfig_2.0.3 diff --git a/articles/index.html b/articles/index.html index e4961c08..5d2d75d8 100644 --- a/articles/index.html +++ b/articles/index.html @@ -17,7 +17,7 @@ QFeatures - 1.15.1 + 1.15.2 diff --git a/authors.html b/authors.html index 7203b09f..3d6a07a6 100644 --- a/authors.html +++ b/authors.html @@ -17,7 +17,7 @@ QFeatures - 1.15.1 + 1.15.2 @@ -83,13 +83,13 @@

Citation

Gatto L, Vanderaa C (2024). QFeatures: Quantitative features for mass spectrometry data. -R package version 1.15.1, https://github.com/RforMassSpectrometry/QFeatures. +R package version 1.15.2, 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 1.15.1},
+  note = {R package version 1.15.2},
   url = {https://github.com/RforMassSpectrometry/QFeatures},
 }
diff --git a/favicon-16x16.png b/favicon-16x16.png index adbbe594..c6282a7f 100644 Binary files a/favicon-16x16.png and b/favicon-16x16.png differ diff --git a/favicon-32x32.png b/favicon-32x32.png index d6c70e52..2b0bc39d 100644 Binary files a/favicon-32x32.png and b/favicon-32x32.png differ diff --git a/index.html b/index.html index e6cecf57..2d29c189 100644 --- a/index.html +++ b/index.html @@ -40,7 +40,7 @@ QFeatures - 1.15.1 + 1.15.2 diff --git a/news/index.html b/news/index.html index 72b1e06b..6725b412 100644 --- a/news/index.html +++ b/news/index.html @@ -17,7 +17,7 @@ QFeatures - 1.15.1 + 1.15.2 @@ -66,11 +66,15 @@

Changelog

QFeatures 1.15

-

QFeatures 1.15.1

+

QFeatures 1.15.2

+
  • New API unit test (see issue #214.
    • +
+
+

QFeatures 1.15.1

-

QFeatures 1.15.0

+

QFeatures 1.15.0

  • New Bioc devel
diff --git a/pkgdown.yml b/pkgdown.yml index fbf8c704..e6bdd713 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -1,9 +1,9 @@ pandoc: 3.1.13 pkgdown: 2.0.9.9000 -pkgdown_sha: 2db8f2e00e546e6a311b72c0219f3d2006c59892 +pkgdown_sha: 102bcd7ff94ba8cd63f251fad095476f7ea1023a articles: Processing: Processing.html QFeatures: QFeatures.html Visualization: Visualization.html -last_built: 2024-05-08T21:20Z +last_built: 2024-05-13T21:48Z diff --git a/reference/AllGenerics.html b/reference/AllGenerics.html index fc59e56c..910455df 100644 --- a/reference/AllGenerics.html +++ b/reference/AllGenerics.html @@ -17,7 +17,7 @@ QFeatures - 1.15.1 + 1.15.2 diff --git a/reference/AssayLinks.html b/reference/AssayLinks.html index d9423fcc..0462bdc3 100644 --- a/reference/AssayLinks.html +++ b/reference/AssayLinks.html @@ -19,7 +19,7 @@ QFeatures - 1.15.1 + 1.15.2 diff --git a/reference/QFeatures-aggregate.html b/reference/QFeatures-aggregate.html index d75409fa..39c40b9d 100644 --- a/reference/QFeatures-aggregate.html +++ b/reference/QFeatures-aggregate.html @@ -30,7 +30,7 @@ QFeatures - 1.15.1 + 1.15.2 diff --git a/reference/QFeatures-class.html b/reference/QFeatures-class.html index b1e282e9..78641da0 100644 --- a/reference/QFeatures-class.html +++ b/reference/QFeatures-class.html @@ -41,7 +41,7 @@ QFeatures - 1.15.1 + 1.15.2 diff --git a/reference/QFeatures-filtering.html b/reference/QFeatures-filtering.html index 60e20a7f..ecb9f4ef 100644 --- a/reference/QFeatures-filtering.html +++ b/reference/QFeatures-filtering.html @@ -21,7 +21,7 @@ QFeatures - 1.15.1 + 1.15.2 diff --git a/reference/QFeatures-missing-data.html b/reference/QFeatures-missing-data.html index 4c2c5b9c..e28f52ad 100644 --- a/reference/QFeatures-missing-data.html +++ b/reference/QFeatures-missing-data.html @@ -45,7 +45,7 @@ QFeatures - 1.15.1 + 1.15.2 diff --git a/reference/QFeatures-processing.html b/reference/QFeatures-processing.html index 84d358e2..1f29fb2c 100644 --- a/reference/QFeatures-processing.html +++ b/reference/QFeatures-processing.html @@ -35,7 +35,7 @@ QFeatures - 1.15.1 + 1.15.2 diff --git a/reference/QFeatures-subsetBy.html b/reference/QFeatures-subsetBy.html index 2f2f8aa5..26cb4225 100644 --- a/reference/QFeatures-subsetBy.html +++ b/reference/QFeatures-subsetBy.html @@ -25,7 +25,7 @@ QFeatures - 1.15.1 + 1.15.2 diff --git a/reference/countUniqueFeatures.html b/reference/countUniqueFeatures.html index bc0f7bf5..6e861b63 100644 --- a/reference/countUniqueFeatures.html +++ b/reference/countUniqueFeatures.html @@ -20,7 +20,7 @@ QFeatures - 1.15.1 + 1.15.2 diff --git a/reference/display.html b/reference/display.html index 519a75a5..3dd988c5 100644 --- a/reference/display.html +++ b/reference/display.html @@ -24,7 +24,7 @@ QFeatures - 1.15.1 + 1.15.2 diff --git a/reference/feat1.html b/reference/feat1.html index 5de5c5f3..0b87181e 100644 --- a/reference/feat1.html +++ b/reference/feat1.html @@ -22,7 +22,7 @@ QFeatures - 1.15.1 + 1.15.2 diff --git a/reference/feat3.html b/reference/feat3.html index dd7bea6c..63fb4b10 100644 --- a/reference/feat3.html +++ b/reference/feat3.html @@ -33,7 +33,7 @@ QFeatures - 1.15.1 + 1.15.2 diff --git a/reference/hlpsms.html b/reference/hlpsms.html index 6a3785cc..13834ec6 100644 --- a/reference/hlpsms.html +++ b/reference/hlpsms.html @@ -52,7 +52,7 @@ QFeatures - 1.15.1 + 1.15.2 diff --git a/reference/impute.html b/reference/impute.html index ce8047ee..716adc26 100644 --- a/reference/impute.html +++ b/reference/impute.html @@ -24,7 +24,7 @@ QFeatures - 1.15.1 + 1.15.2 @@ -169,8 +169,8 @@

Examples

#> Loading required package: mvtnorm #> Loading required package: Matrix #> -#> Attaching package: 'Matrix' -#> The following object is masked from 'package:S4Vectors': +#> Attaching package: ‘Matrix’ +#> The following object is masked from ‘package:S4Vectors’: #> #> expand #> Loading required package: gmm @@ -182,8 +182,8 @@

Examples

#> and has been superseded by the norm2 package. #> Loading required package: pcaMethods #> -#> Attaching package: 'pcaMethods' -#> The following object is masked from 'package:stats': +#> Attaching package: ‘pcaMethods’ +#> The following object is masked from ‘package:stats’: #> #> loadings #> Loading required package: impute diff --git a/reference/index.html b/reference/index.html index 40bd24e3..1a69c024 100644 --- a/reference/index.html +++ b/reference/index.html @@ -17,7 +17,7 @@ QFeatures - 1.15.1 + 1.15.2 @@ -63,50 +63,86 @@

Reference

- + + + - + - - + + - + + + + + + + - + - - + + - + - - + + @@ -118,23 +154,11 @@

All functions hlpsms

- - - - - - - - - + @@ -142,6 +166,14 @@

All functions unfoldDataFrame()

+ + +
-

All functions

-

+

QFeatures class

+

The QFeatures class
-

AllGenerics

+

QFeatures() show(<QFeatures>) plot(<QFeatures>) `[`(<QFeatures>,<ANY>,<ANY>,<ANY>) `[`(<QFeatures>,<character>,<ANY>,<ANY>) c(<QFeatures>) dims(<QFeatures>) nrows(<QFeatures>) ncols(<QFeatures>) rowData(<QFeatures>) `rowData<-`(<QFeatures>,<DataFrameList>) `rowData<-`(<QFeatures>,<ANY>) rbindRowData() selectRowData() rowDataNames() `names<-`(<QFeatures>,<character>) longFormat() addAssay() removeAssay() replaceAssay() `[[<-`(<QFeatures>,<ANY>,<ANY>) updateObject(<QFeatures>) dropEmptyAssays()

Placeholder for generics functions documentation

Quantitative MS QFeatures

+

joinAssays()

+

Join assays in a QFeatures object

show(<AssayLink>) updateObject(<AssayLinks>) updateObject(<AssayLink>) AssayLink() AssayLinks() assayLink() assayLinks() `[`(<AssayLink>,<character>,<ANY>,<ANY>) `[`(<AssayLinks>,<list>,<ANY>,<ANY>) addAssayLink() addAssayLinkOneToOne()

Links between Assays
-

aggregateFeatures(<QFeatures>) aggregateFeatures(<SummarizedExperiment>) adjacencyMatrix(<QFeatures>) `adjacencyMatrix<-`() aggcounts(<SummarizedExperiment>)

+

countUniqueFeatures()

Aggregate an assay's quantitative features

Count Unique Features
-

QFeatures() show(<QFeatures>) plot(<QFeatures>) `[`(<QFeatures>,<ANY>,<ANY>,<ANY>) `[`(<QFeatures>,<character>,<ANY>,<ANY>) c(<QFeatures>) dims(<QFeatures>) nrows(<QFeatures>) ncols(<QFeatures>) rowData(<QFeatures>) `rowData<-`(<QFeatures>,<DataFrameList>) `rowData<-`(<QFeatures>,<ANY>) rbindRowData() selectRowData() rowDataNames() `names<-`(<QFeatures>,<character>) longFormat() addAssay() removeAssay() replaceAssay() `[[<-`(<QFeatures>,<ANY>,<ANY>) updateObject(<QFeatures>) dropEmptyAssays()

+

display()

Quantitative MS QFeatures

-

VariableFilter() filterFeatures(<QFeatures>,<AnnotationFilter>) filterFeatures(<QFeatures>,<formula>)

+

Interactive MultiAssayExperiment Explorer

+

Data import

+

Create QFeatures and SummarizedExperiment object

+
+

readSummarizedExperiment() readQFeatures()

Filter features based on their rowData

QFeatures from tabular data
+

readQFeaturesFromDIANN()

+

Read DIA-NN output as a QFeatures objects

+

Missing data

+

Filtering and handling of missing values

+

zeroIsNA(<SummarizedExperiment>,<missing>) zeroIsNA(<QFeatures>,<integer>) zeroIsNA(<QFeatures>,<numeric>) zeroIsNA(<QFeatures>,<character>) infIsNA(<SummarizedExperiment>,<missing>) infIsNA(<QFeatures>,<integer>) infIsNA(<QFeatures>,<numeric>) infIsNA(<QFeatures>,<character>) nNA(<SummarizedExperiment>,<missing>) nNA(<QFeatures>,<integer>) nNA(<QFeatures>,<numeric>) nNA(<QFeatures>,<character>) filterNA(<SummarizedExperiment>) filterNA(<QFeatures>)

Managing missing data
+

impute impute(<SummarizedExperiment>) impute(<QFeatures>)

+

Quantitative proteomics data imputation

+

QFeatures processing

+

Quantitative data processing

+

logTransform(<SummarizedExperiment>) logTransform(<QFeatures>) scaleTransform(<SummarizedExperiment>) scaleTransform(<QFeatures>) normalize(<SummarizedExperiment>) normalize(<QFeatures>) sweep(<SummarizedExperiment>) sweep(<QFeatures>)

QFeatures processing

-

subsetByFeature subsetByFeature,QFeatures,character-method

+
+

Feature aggregations

+

Feature aggregations

+
+

aggregateFeatures(<QFeatures>) aggregateFeatures(<SummarizedExperiment>) adjacencyMatrix(<QFeatures>) `adjacencyMatrix<-`() aggcounts(<SummarizedExperiment>)

Subset by feature name

-

countUniqueFeatures()

+

Aggregate an assay's quantitative features

+

Filtering

+

Feature filtering

+
+

VariableFilter() filterFeatures(<QFeatures>,<AnnotationFilter>) filterFeatures(<QFeatures>,<formula>)

Count Unique Features

Filter features based on their rowData
-

display()

+

subsetByFeature subsetByFeature,QFeatures,character-method

Interactive MultiAssayExperiment Explorer

+

Subset by feature name

+

Example data

+

Example data

+

feat1

Feature example data

hyperLOPIT PSM-level expression data

-

impute impute(<SummarizedExperiment>) impute(<QFeatures>)

-

Quantitative proteomics data imputation

-

joinAssays()

-

Join assays in a QFeatures object

-

readSummarizedExperiment() readQFeatures()

-

QFeatures from tabular data

-

readQFeaturesFromDIANN()

-

Read DIA-NN output as a QFeatures objects

+
+

DataFrame

+

DataFrame functions

+

reduceDataFrame() expandDataFrame()

Reduces and expands a DataFrame

Unfold a data frame

+

Generic functions

+

Package generics

+
+

AllGenerics

+

Placeholder for generics functions documentation
diff --git a/reference/readQFeatures.html b/reference/readQFeatures.html index b0fa551f..c95dfe7b 100644 --- a/reference/readQFeatures.html +++ b/reference/readQFeatures.html @@ -32,7 +32,7 @@ QFeatures - 1.15.1 + 1.15.2 diff --git a/reference/readQFeaturesFromDIANN.html b/reference/readQFeaturesFromDIANN.html index 7da14788..2b89bbfc 100644 --- a/reference/readQFeaturesFromDIANN.html +++ b/reference/readQFeaturesFromDIANN.html @@ -21,7 +21,7 @@ QFeatures - 1.15.1 + 1.15.2 diff --git a/reference/reduceDataFrame.html b/reference/reduceDataFrame.html index 1107f1a5..73b4642a 100644 --- a/reference/reduceDataFrame.html +++ b/reference/reduceDataFrame.html @@ -26,7 +26,7 @@ QFeatures - 1.15.1 + 1.15.2 diff --git a/reference/unfoldDataFrame.html b/reference/unfoldDataFrame.html index 6018631c..21a10af8 100644 --- a/reference/unfoldDataFrame.html +++ b/reference/unfoldDataFrame.html @@ -84,7 +84,7 @@ QFeatures - 1.15.1 + 1.15.2