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())
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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.
1 2 3 4 5 | 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)
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