# Quantitative features for mass spectrometry data

## Documentation for package ‘QFeatures’ version 1.2.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

addAssay | Quantitative MS QFeatures
addAssayLink | Links between Assays
addAssayLinkOneToOne | Links between Assays
aggcounts | Aggregate an assay's quantitative features
aggcounts,SummarizedExperiment | Aggregate an assay's quantitative features
aggcounts-method | Aggregate an assay's quantitative features
aggregateFeatures | Aggregate an assay's quantitative features
aggregateFeatures-method | Aggregate an assay's 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
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
countUniqueFeatures | Count Unique Features This function counts the number of unique features per sample. A grouping structure can be provided to count higher level features from assays, for example counting the number of unique proteins from PSM data.
dims-method | Quantitative MS QFeatures
display | Interactive MultiAssayExperiment Explorer
expandDataFrame | Reduces and expands a 'DataFrame'
feat1 | Feature example data
feat2 | Feature example data
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
hlpsms | hyperLOPIT PSM-level expression data
impute | Quantitative proteomics data imputation
impute-method | Quantitative proteomics data imputation
infIsNA | Managing missing data
infIsNA-method | Managing missing data
joinAssays | Join assays in a QFeatures object
logTransform | QFeatures processing
logTransform-method | QFeatures processing
longFormat | Quantitative MS QFeatures
missing-data | Managing missing data
names<--method | Quantitative MS QFeatures
nNA | Managing missing data
nNA-method | Managing missing data
normalize | QFeatures processing
normalize-method | QFeatures processing
normalizeMethods | QFeatures processing
NumericVariableFilter | Filter features based on their rowData
NumericVariableFilter-class | Filter features based on their rowData
QFeatures | Quantitative MS QFeatures
QFeatures-class | Quantitative MS QFeatures
QFeatures-filtering | Filter features based on their rowData
QFeatures-processing | QFeatures processing
readQFeatures | QFeatures from tabular data
readSummarizedExperiment | QFeatures from tabular data
reduceDataFrame | Reduces and expands a 'DataFrame'
removeRowDataCols | Quantitative MS QFeatures
replaceRowDataCols | Quantitative MS QFeatures
rowData-method | Quantitative MS QFeatures
rowDataNames | Quantitative MS QFeatures
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
VariableFilter | Filter features based on their rowData
zeroIsNA | Managing missing data
zeroIsNA-method | Managing missing data
[-method | Links between Assays
[-method | Quantitative MS QFeatures