plotDist: plotDist

In chrisamiller/readDepth: Find regions of genomic copy number loss and gain from short reads

Description

plot overlapping histograms of the model distribution and the actual distribution of reads

Usage

  plotDist(rdo,xmax,filename,windSize)

Arguments

rdo	a readDepth object created with new("rdObject")
xmax	the scale of the xaxis goes from 0 until this value (default 2000)
filename	the output file (default "output/hist.pdf")
windSize	the window size for the histogram to use (default 20)

Value

a histogram that helps determine how well the model fits the data

Examples

  ##get regions of CN gain and loss
  #  rdo <- readDepth(x)

  ##does the model fit well
  #  plotDist(rdo)

  ##does it fit better after mapability correction?
  #  rdo2 = rd.mapCorrect(rdo)
  #  plotDist(rdo2)
  
  ##adjust the graphical params for a different view
  #  plotDist(rdo2, 1000, "output/postMapCorrect.pdf", 10)

chrisamiller/readDepth documentation built on June 16, 2021, 2:05 p.m.