sort_counts: Sort columns of a count matrix by rows in sample data

In HuntsmanCancerInstitute/hciR: RNA-seq workflows at HCI

Sort columns of a count matrix by rows in sample data

Description

DESeqDataSetFromMatrix requires count columns sorted by the rows in sample data and only checks if sample row names match count column names (and tibbles do not have row names). This matches column names in a count table to the first column in sample data and reorders columns to match.

Usage

sort_counts(count_tbl, sample_tbl, id = 1)

Arguments

count_tbl	count matrix, data.frame or tibble
sample_tbl	sample tabl with a column containing the columns names in count matrix
id	position of column in sample data that matches column names in the count table, default is the first column

Value

A count matrix with columns re-ordered to match the sample table

Author(s)

Chris Stubben

Examples

## Not run: 
count_tbl <-  sort_counts(counts, samples)

## End(Not run)

HuntsmanCancerInstitute/hciR documentation built on Dec. 10, 2024, 12:22 p.m.