Custom wrapper for fora.
Usage
fora2(
pathways,
genes,
universe,
gene_column = "entrez_gene",
minSize = 1,
maxSize = length(universe) - 1,
adjust.method = "scale",
adjust.globally = TRUE
)Arguments
- pathways
output of
link{msigdbr2}.- genes
named list of genes. These are usually clusters of related genes.
- universe
character vector of background genes. Usually, this is all unique elements of
genes.- gene_column
character; the name of the column in pathways containing the elements of each gene set.
- minSize
integer; minimum size of gene sets allowed for testing.
- maxSize
integer; maximum size of gene sets allowed for testing.
- adjust.method
character string; p-value correction method. Either "scale" (default), which will compute scaled p-values or one of
p.adjust.methods.- adjust.globally
logical; should p-values from all contrasts be adjusted together using
adjust.method? Set toFALSEif the contrasts being tested are not closely related.
Details
If adjust.method = "scale", the function will calculate the
maximum overlap for each combination of names(genes) and (if
adjust.globally = TRUE), the entries of the "gs_subcat" column of
pathways. For each gene set, it will then calculate the ratio of the
size of that set's overlap to one plus the maximum overlap. The addition of
1 in the denominator is to penalize small maximum overlaps. The
log10(pval) is multiplied by this overlap ratio and then
back-transformed to obtain p-values adjusted by how well they describe each
group defined by genes.