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SwathXtend (version 1.0.0)

SWATH extended library generation and satistical data analysis

Description

It contains utility functions for integrating spectral libraries for SWATH and statistical data analysis for SWATH generated data.

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Version

Version

1.0.0

License

GPL-2

Maintainer

Jemma Wu

Last Published

February 15th, 2017

Functions in SwathXtend (1.0.0)

checkQuality

Checking for the integration quality of two libraries
canonicalFormat

Standardise a sprectrum library data frame
buildSpectraLibPair

Build a spectra library by integrating a pair of spectrum libraries
applyttestPep

Function to apply t-test separately for all peptides of each protein
medianNorm

Utility to median normalize a matrix by columns
cleanLib

Spectrum library cleanining
mlrGroup

Function to do mlr normalization for a matrix group
applyttest

Utility to apply a t-test to all rows of a matrix
ionCorGS

Gold standard relative ion intensity correlation (spearman)
mlr

Function to implement mlr normalization
plotRTResd

Plot residuals for retention time prediction of two libraries
plotRTCor

Plot for retention time correlation of two libraries
readLibFile

Load a spectrum library into a data frame
plotRelativeDensities

Plotting utility to overlay all relative densities
outputLib

output a spectrum library into a PeakView format file
mlrrep

Function to do mlr normalizatiopn on a matrix of replicates
plotAll

Plot statistical plots for two libraries
plotDensities

Utility to do side by side density plots
plotRIICor

Plot relative ion intensity correlation of two libraries
plotErrorBarsLines

Utility for clustering plots to plot lines and an overall trend