SeedMatchR (version 1.1.1)

filter_deseq: Filter DESEQ2 Results for SeedMatchR

Description

Filter DESeqDataSet results for use with seed matching and counting functions.

The filtering criteria are:

Filter out genes that are not expressed or counted at all: baseMean = 0 & pvalue = NA & log2FoldChange = NA

Filter out genes that are expressed, but there is not difference across groups: log2FoldChange = 0

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

Remove NA gene_ids and log2FoldChange values

Usage

filter_deseq(
  res,
  fdr.cutoff = 1,
  fc.cutoff = 0,
  rm.na.name = FALSE,
  rm.na.log2fc = FALSE,
  baseMean.cutoff = 0
)

Value

A modified DESEQ2 results table that has been filtered

Arguments

res

The DESEQ2 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.

rm.na.name

Remove na values from the gene_name column

rm.na.log2fc

Remove na values from the log2FoldChange column

baseMean.cutoff

The minimum baseMean expression cutoff

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 DESeq2 results for SeedMatchR
res = filter_deseq(res, fdr.cutoff=1, fc.cutoff=0, rm.na.log2fc = TRUE)
}