deseq2_analysis: DESeq2 analysis

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

DESeq2 analysis

Description

DESeq2 analysis

Usage

deseq2_analysis(txi, design, formula, filter = 2, count_matrix = NULL, ...)

Arguments

txi	The txi object returned by the import_kallisto function.
design	The experimental design (see ?DESeqDataSetFromTximport).
formula	The design formula in data.frame format (see ?DESeqDataSetFromTximport).
filter	The minimum number of reads detected for a feature across all samples. Default: 2
count_matrix	Use an alternative count matrix to use for the differential analysis instead of txi$counts. Will use the DESeq2::DESeqDataSetFromMatrix instead of the DESeq2::DESeqDataSetFromTximport function, so will work even if txi object is incomplete (i.e.: length matrix is missing). Default: NA.
...	Extra param for the DESeq2::DESeq function

Value

A DESeqDataSet object.

Examples

txi <- get_demo_txi()
design <- get_demo_design()
dds <- deseq2_analysis(txi, design, ~ group)
de <- DESeq2::results(dds, contrast = c("group", "A", "B"))

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