Skip to contents

Summarize RNA-seq expression results

Source: R/summarize-dge.R
summarize_dge.Rd

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)
#>     Direction    N Percent
#> 1          Up 2376   21.60
#> 2        Down 3020   27.45
#> 3 Unperturbed 5606   50.95