format_de_odysse: Prepare formated DE table in odysse format.

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

Prepare formated DE table in odysse format.

Description

The table contains annotation and the DE results. The de_res input object must be annotated and correctly formatted (i.e.: from produce_deliverables

Usage

format_de_odysse(de_res, txi, samples_grp1, samples_grp2, digits = 4)

Arguments

de_res	The results from DESeq2::results converted to data.frame.
txi	The txi object returned by the import_kallisto function.
digits	Integer indicating the number of decimal places
contrast	The contrast for the comparison (see ?DESeq2::results).
design_group	The column from the design where the contrasts are located. Default: "group"
ignoreTxVersion	Should the transcript version be ignored for anno mapping. Default: FALSE.

Value

A data.frame with the anno and the merged counts values.

Examples

txi <- get_demo_txi()
design <- get_demo_design()
dds <- deseq2_analysis(txi, design, ~ group)
de_res <- format_de_results(dds, txi, c("group", "A", "B"))
samples_grp1 <- design[design$group == "A",]$sample
samples_grp2 <- design[design$group == "B",]$sample
de <- format_de_odysse(de_res, txi, samples_grp1, samples_grp2)

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