hist.LFRset: Plotting histograms on an LFR data set

In chedonat/DigitalPicoTools: DIGITAL ANALYSIS OF PICOGRAM QUANTITIES OF DNA

Description

This is a generic function to plot the histogram of the Length or the Average coverage of the long Frangment Reads within an LFR data set. given the paramter value, two values can be plotted: The fragment length and the fragment average coverage

Usage

## S3 method for class 'LFRset'
hist(object, value = "Coverage", minlength = 10000,
  color = "black", main = "", well = NULL)

Arguments

minlength	Minimum length of a fragment to be considered. Default 10000.
color	histogram color. default: black
main	The title of the plot. default: None
x	an LFRset object containing the list of Long Fragment Reads
Value	The variable to plot the histogram for . Can be either 'Coverage' either 'length'. default is 'Coverage'.

Value

”

See Also

plotLFRDistribution, plot.LFRset, getWells, getWellLFRset, getLFRStats

Examples

 #Example 1:
 wellsID_file=system.file('extdata','wells_id_tissue.txt',package='DigitalPicoTools')
 wellsID_list<-unlist(read.table(wellsID_file))
 WellSample_list=initsWellSamples(wellsID_list,
     BAMprefix=paste(path.package('DigitalPicoTools'),'extdata/',sep='/'))
 LFR_Info = getLFRset(WellSample_list,3000)
 well1=getWellLFRset(LFR_Info,1)
 hist(well1,value='Length')
 hist(LFR_Info,value='Coverage', color='magenta',main='test')

chedonat/DigitalPicoTools documentation built on May 13, 2019, 3:39 p.m.