Generate Reads Profile with deepTools.

ReadProfile(
  bw.folder,
  up.dist = 3000,
  down.dist = 3000,
  species = c("Human", "Mouse", "Rat", "Fly", "Arabidopsis", "Yeast", "Zebrafish",
    "Worm", "Bovine", "Pig", "Chicken", "Rhesus", "Canine", "Xenopus", "Anopheles",
    "Chimp", "E coli strain Sakai", "Myxococcus xanthus DK 1622"),
  gtf.file = NULL,
  compute.matrix.paras = "-p 2",
  plot.heatmap.paras = "--whatToShow 'heatmap and colorbar'",
  deeptools.path = NULL,
  out.folder = NULL,
  out.format = c("pdf", "png", "eps", "svg")
)

Arguments

bw.folder	Folder contains bigWig files.
up.dist	The upstream distance from the TSS. Default: 3000bp.
down.dist	The downstream distance from the TSS. Default: 3000bp.
species	Species used, chosen from "Human","Mouse","Rat","Fly","Arabidopsis","Yeast","Zebrafish","Worm","Bovine","Pig","Chicken","Rhesus", "Canine","Xenopus","Anopheles","Chimp","E coli strain Sakai","Myxococcus xanthus DK 1622". Default: "Human".
gtf.file	GTF file used to create TxDb object. Useful when specie you used is not available in `species`. Default: NULL.
compute.matrix.paras	Parameters for deepTools `computeMatrix`. Default: "-p 2".
plot.heatmap.paras	Parameters for deepTools `plotHeatmap`. Default: "--whatToShow 'heatmap and colorbar'".
deeptools.path	Path contains `computeMatrix` and `plotHeatmap`. Default: NULL (conduct automatic detection).
out.folder	Output folder. Default: NULL (current working directory).
out.format	Output heatmap format. Choose from pdf, png, eps and svg. Default: pdf.

Value

NULL.

Examples

# library(DEbPeak)
# ReadProfile(bw.folder = path/to/bigWigs, species = "Mouse", deeptools.path = "~/anaconda3/bin")