getContrastResults: Get differential statistics results

In crukci-bioinformatics/qPLEXanalyzer: Tools for quantitative proteomics data analysis

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)

crukci-bioinformatics/qPLEXanalyzer documentation built on Oct. 23, 2023, 2:27 a.m.