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 1.10.0 Index]