getContrastResults {qPLEXanalyzer}R Documentation

Get differential statistics results

Description

Get differential statistics results for given contrasts.

Usage

getContrastResults(diffstats, contrast, controlGroup = NULL, transform = TRUE, writeFile= FALSE)

Arguments

diffstats

list; output of computeDiffStats function

contrast

character; contrast of interest for which to retrieve differential statistics results

controlGroup

character; control group such as IgG

transform

logical; apply log2 transformation to the raw intensities

writeFile

logical; whether to write the results into a text file

Value

A data.frame object and text file containing the result of the differential statistics.

Examples

data(human_anno)
data(exp3_OHT_ESR1)
MSnSet_data <- convertToMSnset(exp3_OHT_ESR1$intensities_qPLEX1, metadata=exp3_OHT_ESR1$metadata_qPLEX1,
indExpData=c(7:16), Sequences=2, Accessions=6)
MSnset_norm <- groupScaling(MSnSet_data, scalingFunction=median)
MSnset_Pnorm <- summarizeIntensities(MSnset_norm, sum, human_anno)
contrasts <- c(tam.24h_vs_vehicle = "tam.24h - vehicle")
diffstats <- computeDiffStats(MSnset_Pnorm, contrasts=contrasts)
diffexp <- getContrastResults(diffstats=diffstats, contrast=contrasts)

[Package qPLEXanalyzer version 1.0.4 Index]