getContrastResults {qPLEXanalyzer} | R Documentation |
Get differential statistics results for given contrasts.
getContrastResults( diffstats, contrast, controlGroup = NULL, transform = TRUE, writeFile = FALSE )
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 |
A data.frame
object and text file containing the
result of the differential statistics.
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)