TEQC (Target Enrichment Quality Control, R package) : Clarification on paired-end reads

Question

[bioinfo8]

Hi,

I am using TEQC for analysis of my paired-end bam files.

If I use pairedend = TRUE in the following:

TEQCreport(sampleName = "", targetsName = "", referenceName = "", destDir = "TEQCreport", reads = get.reads(), targets = get.targets(), pairedend = TRUE,  genomesize= 12345678, k=c(1, 2, 3, 5, 10, 20), covthreshold = 8, CovUniformityPlot = TRUE, CovTargetLengthPlot = TRUE, CovGCPlot = TRUE, duplicatesPlot = TRUE, figureFormat = c("jpeg", "png", "tiff"))

1) Is it equivalent to the following three commands or I have to remove singleReads separately for all my bam files?:

reads <- get.reads("myBAM.bam", filetype="bam")
readpairs <- reads2pairs(reads)
reads <- reads[!(reads$ID %in% readpairs$singleReads$ID), , drop=TRUE]

2) If yes, then the parameters mentioned below would consider only readpairs (no single reads)?

CovUniformityPlot = TRUE, CovTargetLengthPlot = TRUE, CovGCPlot = TRUE, duplicatesPlot = TRUE

3) If no, how can I incorporate those three commands in TEQCreport()?

Kindly guide. Thanks!