ave.mean.median: This function plots pileups of each selected chromosome

In gb305/Rpackages:

Description

This function plots pileups of each selected chromosome

Usage

ave.mean.median(
  aveType,
  aveLArg,
  rc,
  pT,
  arrowsYes = 0,
  offsetf = 1,
  noReflect = 1
)

Arguments

aveType	Average type mean or median
aveLArg	A list of chromosomes
pT	A list of plot titles
arrowsYes	Boolean. 1 = arrows at CHiP sights, 2 = no arrows
offsetf	The plot offset. Default = 1 Path to the input file
noReflect	Boolean.1 No x axis reflection. 0 means x axis reflection

Details

save.mean.median <- function(aveType,aveLArg,rc,pT,arrowsYes=0,offsetf=1, noReflect=1){

if (noReflect != 1){

aveLArg[[1]] = ave.filter(list(aveLArg[[1]],inverse.matrix(aveLArg[[1]])),aveType)

aveLArg[[2]] = ave.filter(list(aveLArg[[2]],inverse.matrix(aveLArg[[2]])),aveType)

}

HiC.Plot(matrix.sparse(aveLArg[[1]]),pT[1],arrowsYes,offsetf)

HiC.Plot(matrix.sparse(aveLArg[[2]]),pT[2],arrowsYes,offsetf)

color.bar(maxC,sz)

HiCRatio.Plot(ratioF(aveLArg[[1]],aveLArg[[2]],rc),pT[3],arrowsYes,offsetf)

ratio.color.bar(colorRampPalette(c("red","white","blue"))(shades*2), ratioSBR,round(ratioSBR+1,0))

}

Value

Plots pileups of selected chromosomes.

gb305/Rpackages documentation built on Feb. 18, 2020, 2:55 p.m.