SwathXtend: SWATH extended library generation and satistical data analysis

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

Author
J WU and D Pascovici
Date of publication
None
Maintainer
Jemma Wu <jwu@proteome.org.au>
License
GPL-2
Version
1.2.0

View on Bioconductor

Man pages

applyttest
Utility to apply a t-test to all rows of a matrix
applyttestPep
Function to apply t-test separately for all peptides of each...
buildSpectraLibPair
Build a spectra library by integrating a pair of spectrum...
canonicalFormat
Standardise a sprectrum library data frame
checkQuality
Checking for the integration quality of two libraries
cleanLib
Spectrum library cleanining
ionCorGS
Gold standard relative ion intensity correlation (spearman)
medianNorm
Utility to median normalize a matrix by columns
mlr
Function to implement mlr normalization
mlrGroup
Function to do mlr normalization for a matrix group
mlrrep
Function to do mlr normalizatiopn on a matrix of replicates
outputLib
output a spectrum library into a PeakView format file
plotAll
Plot statistical plots for two libraries
plotDensities
Utility to do side by side density plots
plotErrorBarsLines
Utility for clustering plots to plot lines and an overall...
plotRelativeDensities
Plotting utility to overlay all relative densities
plotRIICor
Plot relative ion intensity correlation of two libraries
plotRTCor
Plot for retention time correlation of two libraries
plotRTResd
Plot residuals for retention time prediction of two libraries
readLibFile
Load a spectrum library into a data frame

Files in this package

SwathXtend/DESCRIPTION
SwathXtend/NAMESPACE
SwathXtend/R
SwathXtend/R/alignRTbyHydro.R
SwathXtend/R/applyttest.R
SwathXtend/R/applyttestPep.R
SwathXtend/R/buildSpectraLibPair.R
SwathXtend/R/canonicalFormat.R
SwathXtend/R/checkQuality.R
SwathXtend/R/cleanLib.R
SwathXtend/R/computeRIICor.R
SwathXtend/R/computeRTCor.R
SwathXtend/R/consolidateAccession.R
SwathXtend/R/convertAACount.R
SwathXtend/R/getRTrain.R
SwathXtend/R/isMissCleavaged.R
SwathXtend/R/libraryFormat.R
SwathXtend/R/medianNorm.R
SwathXtend/R/mlr.R
SwathXtend/R/mlrGroup.R
SwathXtend/R/mlrrep.R
SwathXtend/R/normalise.R
SwathXtend/R/openSwathFormat.R
SwathXtend/R/outputLib.R
SwathXtend/R/parseAccession.R
SwathXtend/R/plotAll.R
SwathXtend/R/plotDensities.R
SwathXtend/R/plotErrorBarsLines.R
SwathXtend/R/plotRIICor.R
SwathXtend/R/plotRTCor.R
SwathXtend/R/plotRTResd.R
SwathXtend/R/plotRelativeDensities.R
SwathXtend/R/plotStats.R
SwathXtend/R/predictRT.R
SwathXtend/R/proteinOverlap.R
SwathXtend/R/readLibFile.R
SwathXtend/R/selectModel.R
SwathXtend/R/splitData.R
SwathXtend/R/splitLib.R
SwathXtend/build
SwathXtend/build/vignette.rds
SwathXtend/data
SwathXtend/data/ionCorGS.rda
SwathXtend/inst
SwathXtend/inst/doc
SwathXtend/inst/doc/SwathXtend_vignette.R
SwathXtend/inst/doc/SwathXtend_vignette.Rnw
SwathXtend/inst/doc/SwathXtend_vignette.pdf
SwathXtend/inst/files
SwathXtend/inst/files/Lib1.txt
SwathXtend/inst/files/Lib2.txt
SwathXtend/inst/files/Lib3.txt
SwathXtend/inst/files/hydroIndex.txt
SwathXtend/man
SwathXtend/man/applyttest.Rd
SwathXtend/man/applyttestPep.Rd
SwathXtend/man/buildSpectraLibPair.Rd
SwathXtend/man/canonicalFormat.Rd
SwathXtend/man/checkQuality.Rd
SwathXtend/man/cleanLib.Rd
SwathXtend/man/ionCorGS.Rd
SwathXtend/man/medianNorm.Rd
SwathXtend/man/mlr.Rd
SwathXtend/man/mlrGroup.Rd
SwathXtend/man/mlrrep.Rd
SwathXtend/man/outputLib.Rd
SwathXtend/man/plotAll.Rd
SwathXtend/man/plotDensities.Rd
SwathXtend/man/plotErrorBarsLines.Rd
SwathXtend/man/plotRIICor.Rd
SwathXtend/man/plotRTCor.Rd
SwathXtend/man/plotRTResd.Rd
SwathXtend/man/plotRelativeDensities.Rd
SwathXtend/man/readLibFile.Rd
SwathXtend/vignettes
SwathXtend/vignettes/SwathXtend_vignette.Rnw