get_ranking_sharing_index: Get ranking and sharing indexes

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

Get ranking and sharing indexes

Description

This function calculates sharing and ranking indexes for a set of samples and then plots the result.

Usage

get_ranking_sharing_index(
  peak_files,
  bam_files,
  filename = "master_sharing_ranking_index.rds",
  perc_overlap,
  TxDb = TxDb.Hsapiens.UCSC.hg38.knownGene::TxDb.Hsapiens.UCSC.hg38.knownGene,
  nthreads = 2
)

Arguments

peak_files	Character vector with the path of the peak files.
bam_files	Character vector with the path of the bam files.
perc_overlap	Percentage of overlap (from 0 to 1) with a peak in a sample with the master peaklist to consider it an overlap. Default: 0.4
TxDb	TxDb object or GRanges object with the gene annotation to use to classify peaks into Promoters or Distal. Default: TxDb.Hsapiens.UCSC.hg38.knownGene.
nthreads	Number of threads to use for the analysis.

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