sigtools_aggregation: Generates aggregation plots for all the signals in the given...

In shohre73/sigtools: Visualizing Genomic Signals

Description

Generates aggregation plots for all the signals in the given multi-column bedGraph file, over the specified elements in the given interval file

Usage

sigtools_aggregation(
  path_mulColBedG,
  path_reg,
  chr,
  mode,
  header = FALSE,
  prefix = "s",
  sep = "\t",
  outdir = "aggregation",
  resolution = 200L,
  neighborhood = 50L,
  percentile = 100,
  enrichment = FALSE,
  means = c(NA)
)

Arguments

path_mulColBedG	The path to the input multi-column bedgraph file
chr	The intended chromosome (example:21L)
mode	Controls the length unification process [options: 'point' or 'stretch']
header	Does your file include headers? [default:FALSE]
prefix	Your preferred prefix for naming the signals [default:'s']
sep	Your field separator character [default:'\t']
outdir	Name of the output directory [default:aggregation]
resolution	The bin size of the input file [default:200]
neighborhood	The number of covered up and down stream bins [default:50]
percentile	What percentile of your data you want to work with [default:'100']
enrichment	Do you like to plot the enrichment? [default:FALSE]
means	If given, istead of calculating mean values of the signals, the mean will be obtained from this list [default:c(NA)]
path_regThe	The path to the inpput interval file

Examples

sigtools_aggregation(path_mulColBedG = "./test_data/E003-assays_chr21_bin200_bwtool.mcBedGraph", path_reg = "./test_data/Ensembl_chr21.gene_info", chr = 21, mode = 'stretch', header = TRUE , outdir = 'aggregation_E003-chr21_enriched_2', resolution = 200L , neighborhood = 10L, enrichment = TRUE, means = c(0.640, 0.601, 0.633, 0.575, 0.604, 0.597) )

shohre73/sigtools documentation built on April 2, 2021, 4:52 a.m.