count_features: count_features function

In irilenia/baerhunter: Detection and Analysis of Expressed Intergenic Elements in Bacterial RNA-seq Data

count_features function

Description

This is a function to employ Rsubread featureCounts to quantify expression of annotated and predicted elements

Usage

count_features(
  bam_dir = ".",
  annotation_dir = ".",
  annotation_file,
  output_dir = ".",
  output_filename = "dataset",
  chromosome_alias_file,
  strandedness,
  is_paired_end,
  excl_rna = T,
  ...
)

Arguments

bam_dir	The directory where bam files located
annotation_dir	The directory where annotation file is located
annotation_file	The complete annotation file: GFF3 or GTF genome annotation file
output_dir	The full directory path for CSV output files to be written
output_filename	The name for the output files–for example dataset name
chromosome_alias_file	A comma-delimited TXT file containing a character string with the chromosome names. This file has to have two columns: first with the chromosome name in the annotation file, second with the chromosome name in the BAM file.
strandedness	A string outlining the type of the sequencing library: unstranded, stranded, or reversely stranded.
is_paired_end	A boolean indicating if the reads are paired-end.
excl_rna	A boolean indicating if misc RNA features (rRNA, tRNA) are excluded from quantification. (Defaults=T)
...	Optional parameters passed on to featureCounts() Default: allowMultiOverlap = T, fraction = T

Value

Count tables for each feature are written into separate files, as well as the result summary.

irilenia/baerhunter documentation built on May 18, 2024, 11:56 p.m.