signalToNoiseRatio: Signal-to-noise ratio

In mireia-bioinfo/meowmics: What the Package Does (One Line, Title Case)

Signal-to-noise ratio

Description

Given a bam file and peak file, it calculates the signal-to-ratio, that is, the percentage of reads present in called peaks.

Usage

signalToNoiseRatio(
  bam_file,
  peak_file,
  genes = NULL,
  suffix = ".bam",
  build = "hg38",
  promoter_dist = 2000,
  nthreads = 5,
  paired_end = FALSE
)

Arguments

bam_file	Character with the path of the BAM file.
peak_file	Character with the path of the peak file.
genes	Data.frame containing the coding genes to use as annotation, as outputed by the function obtainCodingGenes. If set to NULL (default) it will run the function to recover coding genes.
suffix	Suffix to remove from the bam_file to generate the sample name.
build	Name of the build to use to extract promoter coordinates. Can be either hg38 (default) or hg19.
promoter_dist	Distance from TSS to classify promoter and distal regions.
nthreads	Number of threads to use for counting BAM reads.

Value

Data.frame containing the number and percentage of reads located in promoter peaks, distal peaks and unassigned.

mireia-bioinfo/meowmics documentation built on July 29, 2023, 10 p.m.