makeDiffExprFile {NanoTube} | R Documentation |
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.
makeDiffExprFile( limmaResults, filename = NULL, returns = c("all", "stats"), skip.first = TRUE )
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). |
A table of differential expression results
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")