Filter differential expression results — filter

Filter differential expression results for use with search and counting functions.

The filtering criteria are:

Filter out genes that are not expressed or counted at all: baseMean == NA | pvalue == NA | log2FoldChange == NA

Filter out genes with extreme outliers: pvalue = NA and padj = NA

Filter out genes that have been excluded by independent filtering. padj = NA

Filter results by the fdr_cutoff

Filter the results by the log2FoldChange

Filter the results by the baseMean

Usage

filter_res(res, fdr_cutoff = 1, fc_cutoff = 0, basemean_cutoff = 30)

Arguments

res: The differential expression results as a data frame
fdr_cutoff: The false discovery rate cutoff to use.
fc_cutoff: The fold change cutoff to use. The absolute value will be used as the cutoff and values greater-than-or-equal-to will be kept.
basemean_cutoff: The minimum baseMean expression cutoff

Value

A filtered results data frame

Examples

if (FALSE) { # interactive()
# Load test data
get_example_data("sirna")

sirna.data = load_example_data("sirna")

res <- sirna.data$Schlegel_2022_Ttr_D1_30mkg

# Filter differential expression results for SeedMatchR
res = filter_res(res, fdr_cutoff=1, fc_cutoff=0)
}