Quantitative features for mass spectrometry data

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Documentation for package ‘QFeatures’ version 1.20.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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
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