deseq_from_tibble: Run DESeq from tibbles

In HuntsmanCancerInstitute/hciR: RNA-seq workflows at HCI

Run DESeq from tibbles

Description

Creates DESeqDataSet object using count and sample tibbles as input and optionally runs DESeq

Usage

deseq_from_tibble(counts, samples, run_deseq = TRUE, minReplicates = 7, ...)

Arguments

counts	a count table with feature ids in row 1
samples	a sample table with names matching count table column names in row 1
run_deseq	Run DESeq, default TRUE
minReplicates	minimum number of replicates required in order to use replaceOutliers on a sample, default 7.
...	additional options like the design formula are passed to DESeqDataSetFromMatrix

Value

A DESeqDataSet object

Note

This function first runs sort_counts to check and reorder count columns by the first column in samples, and then DESeqDataSetFromMatrix and optionally DESeq. To match DESeq2 versions < 1.16, set run_deseq = FALSE and then run DESeq(dds, betaPrior =TRUE)'

Author(s)

Chris Stubben

Examples

## Not run: 
   deseq_from_tibble(counts, samples, design = ~ trt)

## End(Not run)

HuntsmanCancerInstitute/hciR documentation built on Aug. 20, 2024, 12:22 a.m.