read_featureCounts: Read featureCounts output files

Description Usage Arguments Value Author(s) Examples

View source: R/read_featureCounts.R

Description

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

Usage

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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

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## 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 6, 2020, 12:40 p.m.