# Quantitative features for mass spectrometry data

## Documentation for package ‘QFeatures’ version 1.22.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

A C D E F H I J L M N P Q R S U V Z misc

## -- A --

addAssay | Quantitative MS QFeatures
addAssayLink | Links between Assays
addAssayLinkOneToOne | Links between Assays
adjacencyMatrix-method | Aggregate assays' quantitative features
adjacencyMatrix<- | Aggregate assays' quantitative features
aggcounts | Aggregate assays' quantitative features
aggcounts-method | Aggregate assays' quantitative features
aggregateFeatures | Aggregate assays' quantitative features
aggregateFeatures-method | Aggregate assays' quantitative features
AllGenerics | Placeholder for generics functions documentation
AssayLink | Links between Assays
assayLink | Links between Assays
AssayLink-class | Links between Assays
AssayLinks | Links between Assays
assayLinks | Links between Assays
AssayLinks-class | Links between Assays

## -- C --

c-method | Quantitative MS QFeatures
CharacterVariableFilter | Filter features based on their rowData
CharacterVariableFilter-class | Filter features based on their rowData
class:AssayLink | Links between Assays
class:AssayLinks | Links between Assays
class:QFeatures | Quantitative MS QFeatures
coerce-method | Quantitative MS QFeatures
coerce-QFeatures | Quantitative MS QFeatures
countUniqueFeatures | Count Unique Features
createPrecursorId | Create precursor identfiers

## -- D --

dims-method | Quantitative MS QFeatures
display | Interactive MultiAssayExperiment Explorer
dropEmptyAssays | Quantitative MS QFeatures

## -- E --

expandDataFrame | Reduces and expands a 'DataFrame'

## -- F --

feat1 | Feature example data
feat2 | Feature example data
feat3 | Example 'QFeatures' object after processing
feat4 | Example 'QFeatures'
filterFeatures | Filter features based on their rowData
filterFeatures-method | Filter features based on their rowData
filterNA | Managing missing data
filterNA-method | Managing missing data
ft_na | Feature example data

## -- H --

hlpsms | hyperLOPIT PSM-level expression data

## -- I --

impute | Quantitative proteomics data imputation
impute-method | Quantitative proteomics data imputation
infIsNA | Managing missing data
infIsNA-method | Managing missing data
isDuplicated | Filter features based on their rowData

## -- J --

joinAssays | Join assays in a QFeatures object

## -- L --

logTransform | QFeatures processing
logTransform-method | QFeatures processing
longForm | Reshape into a long data format
longForm,QFeatures | Reshape into a long data format
longForm,SummarizedExperiment | Reshape into a long data format
longForm-method | Reshape into a long data format
longFormat | Reshape into a long data format

## -- M --

missing-data | Managing missing data

## -- N --

names<--method | Quantitative MS QFeatures
ncols-method | Quantitative MS QFeatures
nNA | Managing missing data
nNA-method | Managing missing data
normalize | QFeatures processing
normalize-method | QFeatures processing
normalizeMethods | QFeatures processing
nrows-method | Quantitative MS QFeatures
NumericVariableFilter | Filter features based on their rowData
NumericVariableFilter-class | Filter features based on their rowData

## -- P --

plot.QFeatures | Quantitative MS QFeatures

## -- Q --

QFeatures | Quantitative MS QFeatures
QFeatures-class | Quantitative MS QFeatures
QFeatures-filtering | Filter features based on their rowData
QFeatures-processing | QFeatures processing

## -- R --

rbindRowData | Quantitative MS QFeatures
readQFeatures | QFeatures from tabular data
readQFeatures,data.frame,data.frame | QFeatures from tabular data
readQFeatures,data.frame,vector | QFeatures from tabular data
readQFeatures,missing,vector | QFeatures from tabular data
readQFeaturesFromDIANN | Read DIA-NN output as a QFeatures objects
readSummarizedExperiment | QFeatures from tabular data
reduceDataFrame | Reduces and expands a 'DataFrame'
removeAssay | Quantitative MS QFeatures
replaceAssay | Quantitative MS QFeatures
replaceColnames | Quantitative MS QFeatures
rowData-method | Quantitative MS QFeatures
rowData<--method | Quantitative MS QFeatures
rowDataNames | Quantitative MS QFeatures

## -- S --

scaleTransform | QFeatures processing
scaleTransform-method | QFeatures processing
selectRowData | Quantitative MS QFeatures
se_na2 | Feature example data
show-method | Links between Assays
show-method | Quantitative MS QFeatures
subsetByFeature | Subset by feature name
subsetByFeature-method | Subset by feature name
sweep | QFeatures processing
sweep-method | QFeatures processing

## -- U --

unfoldDataFrame | Unfold a data frame
updateObject-method | Links between Assays
updateObject-method | Quantitative MS QFeatures

## -- V --

VariableFilter | Filter features based on their rowData

## -- Z --

zeroIsNA | Managing missing data
zeroIsNA-method | Managing missing data

## -- misc --

[-method | Links between Assays
[-method | Quantitative MS QFeatures
[[<--method | Quantitative MS QFeatures