lgatto/Features
Quantitative features for mass spectrometry data

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Functions
206
Source code
38
Man pages
19
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lgatto/Features: Quantitative features for mass spectrometry data
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API

API for lgatto/Features
Quantitative features for mass spectrometry data

Global functions
.addDiannExtractedData Source code
.adjacencyMatrix Source code
.aggregateQFeatures Source code
.applyTransformation Source code
.checkAssaysToInsert Source code
.checkFilterVariables Source code
.checkLinksInHits Source code
.checkQuantCols Source code
.checkRunCol Source code
.checkWarnEcol Source code
.combineAssayLinks Source code
.combineAssays Source code
.combineColData Source code
.createUniqueColnames Source code
.create_assay_link Source code
.findPrecursorVariables Source code
.formatColData Source code
.formatMtraqReportData Source code
.get_Hits Source code
.infIsNA Source code
.keepLostAssays Source code
.keepSharedSamples Source code
.merge_2_by_cols Source code
.merge_assays_by_rows Source code
.merge_by_cols Source code
.nNA Source code
.nNAByAssay Source code
.nNAByMargin Source code
.nNAi Source code
.normIndex Source code
.offsetNodes Source code
.plotlyGraph Source code
.pruneAssayLink Source code
.pruneAssayLinks Source code
.pruneHits Source code
.removeEmptyColumns Source code
.row_for_filterNA Source code
.splitSE Source code
.subsetByFeature Source code
.sweep.useAsDefault Source code
.transferData Source code
.unique_row_names Source code
.updateColDataFromAssays Source code
.validAssayLink Source code
.validAssayLinks Source code
.valid_QFeatures Source code
.valid_QFeatures_indices Source code
.zeroIsNA Source code
AllGenerics Man page
AssayLink Man page Source code
AssayLink-class Man page
AssayLinks Man page Source code
AssayLinks-class Man page
CharacterVariableFilter Man page
CharacterVariableFilter-class Man page
NumericVariableFilter Man page
NumericVariableFilter-class Man page
QFeatures Man page Source code
QFeatures-class Man page
QFeatures-filtering Man page
QFeatures-processing Man page
VariableFilter Man page Source code
[,AssayLink,character,ANY,ANY-method Man page
[,AssayLink,character-method Man page
[,AssayLinks,character-method Man page
[,AssayLinks,list,ANY,ANY-method Man page
[,QFeatures,ANY,ANY,ANY-method Man page
[,QFeatures,character,ANY,ANY-method Man page
[[<-,QFeatures,ANY,ANY-method Man page
addAssay Man page Source code
addAssayLink Man page Source code
addAssayLinkOneToOne Man page Source code
adjacencyMatrix,QFeatures-method Man page
adjacencyMatrix,SummarizedExperiment-method Man page
adjacencyMatrix<- Man page
aggcounts Man page
aggcounts,SummarizedExperiment-method Man page
aggregateFeatures Man page
aggregateFeatures,QFeatures-method Man page
aggregateFeatures,SummarizedExperiment-method Man page
assayLink Man page Source code
assayLinks Man page Source code
c,QFeatures-method Man page
class:AssayLink Man page
class:AssayLinks Man page
class:QFeatures Man page
coerce,MultiAssayExperiment,QFeatures-method Man page
coerce-QFeatures Man page
contains Source code
countUniqueFeatures Man page Source code
dims,QFeatures-method Man page
display Man page Source code
dropEmptyAssays Man page Source code
expandDataFrame Man page Source code
feat1 Man page
feat2 Man page
feat3 Man page
filterFeatures Man page
filterFeatures,QFeatures,AnnotationFilter-method Man page
filterFeatures,QFeatures,formula-method Man page
filterFeaturesWithAnnotationFilter Source code
filterFeaturesWithFormula Source code
filterNA Man page
filterNA,QFeatures-method Man page
filterNA,SummarizedExperiment-method Man page
find_assay_with_feature_name Source code
find_assays_from Source code
ft_na Man page
hlpsms Man page
impute Man page
impute,QFeatures-method Man page
impute,SummarizedExperiment-method Man page
infIsNA Man page
infIsNA,QFeatures,character-method Man page
infIsNA,QFeatures,integer-method Man page
infIsNA,QFeatures,missing-method Man page
infIsNA,QFeatures,numeric-method Man page
infIsNA,SummarizedExperiment,missing-method Man page
invariant_col2 Source code
invariant_cols2 Source code
joinAssays Man page Source code
logTransform Man page
logTransform,QFeatures-method Man page
logTransform,SummarizedExperiment-method Man page
longFormat Man page Source code
main_assay Source code
mergeSElist Source code
missing-data Man page
nNA Man page
nNA,QFeatures,character-method Man page
nNA,QFeatures,integer-method Man page
nNA,QFeatures,missing-method Man page
nNA,QFeatures,numeric-method Man page
nNA,SummarizedExperiment,missing-method Man page
names<-,QFeatures,character-method Man page
ncols,QFeatures-method Man page
normalize Man page
normalize,QFeatures-method Man page
normalize,SummarizedExperiment-method Man page
normalizeMethods Man page
nrows,QFeatures-method Man page
number_assays_in_se Source code
plot.QFeatures Man page
rbindRowData Man page Source code
readQFeatures Man page Source code
readQFeatures,data.frame,data.frame Man page
readQFeatures,data.frame,vector Man page
readQFeatures,missing,vector Man page
readQFeaturesFromDIANN Man page Source code
readSummarizedExperiment Man page Source code
reduceDataFrame Man page Source code
removeAssay Man page Source code
replaceAssay Man page Source code
rowData,QFeatures-method Man page
rowData<-,QFeatures,ANY-method Man page
rowData<-,QFeatures,DataFrameList-method Man page
rowDataNames Man page Source code
scaleTransform Man page
scaleTransform,QFeatures-method Man page
scaleTransform,SummarizedExperiment-method Man page
se_na2 Man page
selectRowData Man page Source code
show,AssayLink-method Man page
show,QFeatures-method Man page
subsetByFeature Man page
subsetByFeature,QFeatures,character-method Man page
sweep Man page
sweep,QFeatures-method Man page
sweep,SummarizedExperiment-method Man page
sweepSE Source code
unfoldDataFrame Man page Source code
updateObject,AssayLink-method Man page
updateObject,AssayLinks-method Man page
updateObject,QFeatures-method Man page
validAdjacencyMatrix Source code
zeroIsNA Man page
zeroIsNA,QFeatures,character-method Man page
zeroIsNA,QFeatures,integer-method Man page
zeroIsNA,QFeatures,missing-method Man page
zeroIsNA,QFeatures,numeric-method Man page
zeroIsNA,SummarizedExperiment,missing-method Man page
lgatto/Features documentation built on April 17, 2024, 3:24 p.m.

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