makeDiffExprFile {NanoTube} | R Documentation

## Make differential expression results file.

### Description

Make a data frame or text file containing coefficients, p-, and q-values from Limma differential expression analysis. If returns == "all", will also center the log-expression data on the median of base.group expression, and include the expression data in the output.

### Usage

    makeDiffExprFile(
      limmaResults,
      filename = NULL,
      returns = c("all", "stats"),
      skip.first = TRUE
    )

### Arguments

`limmaResults` | Result from runLimmaAnalysis
`filename` | The desired name for the output tab-delimited text file. If NULL (default) the resulting table will be returned as an R data frame.
`returns` | If "all" (default), will center the log-expression data on median of base.group expression and include the expression data in the output. If "stats", will only include the differential expression statistics.
`skip.first` | Logical: Skip the first factor for gene set analysis? Frequently the first factor is the 'Intercept', which is generally uninteresting for GSEA (default TRUE).

### Value

A table of differential expression results

### Examples

    data("ExampleResults") # Results from runLimmaAnalysis

    # Include expression data in the results table
    deResults <- makeDiffExprFile(ExampleResults, returns = "all")

    # Only include statistics, and save to a .txt file

    makeDiffExprFile(ExampleResults, file = "DE.txt",
                     returns = "stats")

[Package NanoTube version 1.0.0 Index]