diff_limma_pw_unfiltered: diff_limma_pw_unfiltered (from limma functions).
In ShirinG/exprAnalysis: A package for analysing RNA-seq and expression array data

Description Usage Arguments Value Examples

This calculates the differentially expressed genes among pairwise group comparisons (one comparison at a time) and outputs results for all genes (including non-significant genes).

1 2	diff_limma_pw_unfiltered(expmatrix, design, comparison, p.value = 0.05, lfc = log2(1.5), projectfolder = getwd())

`expmatrix`	An input matrix with gene names as row names and sample names as column names.
`design`	Binary design matrix of samples' treatment groups.
`comparison`	Single comparisons for differential expression analysis.
`p.value`	Significance threshold. Defaults to 0.05
`lfc`	Log fold change threshold. Defaults to 1.5
`projectfolder`	File path where to save the output to. Defaults to working directory. Here, it saves the output to a subfolder called "Diff_limma".

Unfiltered Differential expression output table for the given comparison. The table and Venn diagram are saved to files in the folder "diff_limma" and the table is also returned by the function.

design <- as.matrix(data.frame(Ctrl = c(rep(1, 4), rep(0,12)), TolLPS = c(rep(0, 4), rep(1, 4),
             rep(0, 8)), TollMRP8 = c(rep(0, 8), rep(1, 4), rep(0, 4)), ActLPS = c(rep(0, 12),
             rep(1, 4)), row.names = colnames(expmatrix)))
comparison="TolLPS-Ctrl"
diff_limma_pw_unfiltered_output <- diff_limma_pw_unfiltered(expmatrix, design, comparison)