read_feature_counts: Import read counts from a set of featureCounts files and...

In russHyde/reeq: Provides Some Helper Functions For RNA-Seq Analysis / IO

Description

The files may be of standard format or of short 'featureCounts' format (see below). Only the 'Geneid', 'Length' and counts are kept and the 'Geneid' and 'Length' columns are renamed 'feature_id' and 'length'.

Usage

read_feature_counts(files, sample_ids, comment = "#",
  col_types = "cii", progress = FALSE)

Arguments

files	A vector of file-paths. Each should be an output from 'featureCounts' and contain, at least, the 'Geneid', 'Length' and feature-count columns.
sample_ids	A vector of sample IDs corresponding, in order, to the entries in 'files'. If 'NULL' ...
comment, col_types, progress	Arguments passed through to 'readr::read_tsv' that specify the format of the input files and whether a progress bar should be shown.

Details

Standard format contains: 'Geneid', 'Chr', 'Start', 'End', 'Strand', 'Length', counts

Short format contains: 'Geneid', 'Length', counts

russHyde/reeq documentation built on March 10, 2020, 5:36 a.m.