peak_union_calc: Peak union calculation

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

Peak union calculation

Description

The function goes over each BAM file in the directory and finds the expression peaks that satisfy the coverage boundary and length criteria in each file. Then it unifies the peak information to obtain a single set of peak genomic coordinates.

Usage

peak_union_calc(
  bam_location = ".",
  bam_txt_list = "",
  target_strand,
  low_coverage_cutoff,
  high_coverage_cutoff,
  peak_width,
  paired_end_data = FALSE,
  strandedness = "unstranded"
)

Arguments

bam_location	The directory containing BAM files.
bam_txt_list	Optional newline separated text file of filenames of bam files. File must be located in bam_location directory.
target_strand	A character string indicating the strand. Supports two values; '+' and '-'.
low_coverage_cutoff	An integer indicating the low coverage threshold value.
high_coverage_cutoff	An integer indicating the high coverage threshold value.
peak_width	An integer indicating the minimum peak width.
paired_end_data	A boolean indicating if the reads are paired-end.
strandedness	A string outlining the type of the sequencing library: stranded, or reversely stranded.

Value

An object of IRanges class, containing the genomic coordinates of selected and unified peaks.

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