Description Usage Arguments Value Examples
This calculates the differentially expressed genes among all group comparisons.
1 2 | diff_limma_all(expmatrix, design, groupcomparisons, 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. |
groupcomparisons |
Group 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". |
Differential expression output table for all group comparisons - outputs information for all genes, including non-significant ones.
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)))
groupcomparisons=c("TolLPS-Ctrl", "TollMRP8-Ctrl", "ActLPS-Ctrl")
diff_limma_all_output <- diff_limma_all(expmatrix, design, groupcomparisons)
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