split_de_results: Split differential expression results

In CharlesJB/rnaseq: Wrapper Functions for RNA-Seq Post-Processing

Split differential expression results

Description

This function will split the DE results table into 4 elements: 1) de: The original DE table 2) signif: All the genes considered statistically differentially expressed 3) up: The significant genes that are up-regulated 4) down: The significant genes that are down-regulated

Usage

split_de_results(
  de_res,
  p_threshold = 0.05,
  fc_threshold = 1.5,
  tpm_threshold = NULL
)

Arguments

de_res	the data.frame object returned by the format_de_results function.
p_threshold	The threshold of p stat to be considered as significant. Default: 1.5
fc_threshold	The threshold of FC to be considered as significant. Default: 0.05
tpm_threshold	The threshold of the mean TPM of the current samples to be considered as significant

Details

To be considered significant, a gene must have a padj (qV) value lower or equal to the p_threshold param, an absolute fold change greater or equal to the fc_threshold param. Also, if tpm_threshold is not NULL, the average TPM across all samples in the comparison must be greater or equal to the tpm_threshold value.

It is important to use the results produced with the format_de_results function.

Value

A list of DE tables.

Examples

## Not run: 
txi <- get_demo_txi()
design <- get_demo_design()
dds <- deseq2_analysis(txi, design, ~ group)
de <- format_de_results(dds, txi, c("group", "A", "B"))
split_de <- split_de_results(de)

## End(Not run)

CharlesJB/rnaseq documentation built on Oct. 17, 2023, 5:37 p.m.