summarize_dge: Summarize RNA-seq expression results

In jcalendo/coriell: Convenience Functions for Bioinformatics

Summarize RNA-seq expression results

Description

Summarize a results data.frame. Return data.frame of counts of up/down/non-DE genes based on log-fold-change and significance values.

Usage

summarize_dge(df, fdr_col = "FDR", lfc_col = "logFC", fdr = 0.05, lfc = 0)

Arguments

df	dataframe of results. Must have columns containing significance values and log-fold changes.
fdr_col	Column name of the data.frame containing the significance level values.
lfc_col	Column name of data.frame containing the log-fold change values.
fdr	numeric. FDR or significance value below which genes are considered significant.
lfc	numeric. abs(log-fold change) value above which genes are considered significant.

Value

data.frame with columns describing the count and percentages of up/down/unperturbed genes

Examples

summarize_dge(GSE161650_de)

jcalendo/coriell documentation built on March 5, 2025, 5:42 a.m.