spikeCheck: check the quality of the spike-ins

In BIMSBbioinfo/AmpliconBiSeq: analyzing amplicon bisulfite sequencing data

Description

This function provides methylation statistics for spike-ins. It plots a histogram or set of histograms from spike-in experiments which are helpful to deduce conversion efficiency of the experiment.

Usage

spikeCheck(proj, auxName = "all", sampleName = NULL, coverage = 0,
  targets = NULL, ...)

Arguments

proj	qProject object from QuasR preferably produced by ampBiSeqAlign
auxName	string for which spike-ins should be checked, if equals "all" everything is checked
sampleName	string for which sample the spike-ins should be checked
coverage	minumum coverage before calculation of methylation
targets	named list of GRanges objects identifies targeted regions in given auxiliary genomes
...	arguments to be passed to hist function

Value

a list of percentages of methylated CpGs in all reads.

Examples

# spikeCheck(proj,auxName="all",sampleName="ES.2")
          # spikeCheck(proj,auxName="T7",sampleName="ES.2")

          #la.gr=readRDS("/work2/gschub/Juliane/HTS/QuasRBiSeq/lamdaGR.rds")
          # par(mfrow=c(2,2))
          #spikeCheck(proj,auxName="all",sampleName="ES.2",targets=list(lambda=la.gr))

BIMSBbioinfo/AmpliconBiSeq documentation built on May 5, 2019, 10:25 a.m.