read_featureCounts: Read featureCounts output files

In HuntsmanCancerInstitute/hciR: RNA-seq workflows at HCI

Read featureCounts output files

Description

Reads featureCount count or alignment summary files and optionally reshape into wide format.

Usage

read_featureCounts(path = ".", pattern, reshape = TRUE, stats = FALSE)

Arguments

path	the path to featureCounts output files, the default corresponds to the working directory.
pattern	regular expression for file name matching, default .counts and .summary
reshape	reshape into wide format with samples in rows (count matrix)
stats	read stats tables, default counts

Value

A tibble

Author(s)

Chris Stubben

Examples

## Not run: 
 ft_counts <- read_featureCounts(".")
 fc <- read_featureCounts(".", stats=TRUE)
 fc
 fc <- read_featureCounts(".", stats=TRUE, reshape=FALSE)
 fc
 filter(fc, count!=0) %>%
   hchart("bar", x=sample,  y=count, group=status) %>%
     hc_plotOptions(bar = list(stacking = "normal"))  %>%
      hc_yAxis(reversedStacks = FALSE)

## End(Not run)

HuntsmanCancerInstitute/hciR documentation built on March 26, 2024, 3:09 a.m.