HS.totals: HS.totals

In WHG1990/CCTools: A suite of tools for analysing CC-seq data.

HS.totals

Description

Generates a hotspot table from a full map file or rds set the working directory to the location of the full map files

Usage

HS.totals(
  work.d = getwd(),
  outdir = getwd(),
  Pan,
  use.BG = T,
  readfilename = "FullMap.",
  mode = "txt",
  exp.name = "NA",
  use.mreads = T,
  geneTable =
    "/Users/georgebrown/Dropbox/Annotations/AllElementsDUB_Cer3H4L2_Brar_2016.08.16.txt",
  neeman = F,
  WCequal = F,
  extend = 300
)

Arguments

outdir	output directory
use.BG	whether to use BGreads or not
readfilename	name of the read pattern
exp.name	experiment name
geneTable	location of the AllElementsDUB file
word.d	Working directory where the fullmaps are.

Examples

HS.totals(work.d=getwd(),outdir="/Users/georgebrown/Desktop/foldhsdev"
,Pan="/Users/georgebrown/Dropbox/Annotations/Cer3H4L2/Pan.Hotspots.IGR.SacCer3_H4L2_2016.08.10a.txt")

WHG1990/CCTools documentation built on June 16, 2024, 1:36 a.m.