deseq_from_tibble: Run DESeq from tibbles

Description Usage Arguments Value Note Author(s) Examples

View source: R/deseq_from_tibble.R

Description

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

Usage

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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

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

## End(Not run)

HuntsmanCancerInstitute/hciR documentation built on Jan. 10, 2020, 5:52 p.m.