pileupCounts: Function to obtain the pileup counts for a bam file.

In gamerino/TarSeqQC: TARgeted SEQuencing Experiment Quality Control

Description

pileupCounts waits for a TargetExperiment object containing the bed file information in order to obtain pileup counts only for the specified genomic regions. The resulting object is a data.frame instance, in which each row represents one position of the specified features across the bed file. The first three columns called 'pos', 'seqnames' and 'which_label,' represent the position in the seqnames (e.g. pos=10183795 and seqnames=chr3) and the associated feature. According to the 'pileupP' parameters set before, the number of next columns could change. If 'distinguish_nucleotide' was set to TRUE, then one column per ntd will appear containing the counts obtained for each of them. Same will occur when 'distinguish_strands' is set to TRUE. The last column, called 'counts', contains the total counts obtained for the corresponding position.

Usage

pileupCounts(bed, bamFile, fastaFile, scanBamP = NULL, pileupP = NULL,
    BPPARAM = bpparam())

Arguments

bed	a Granges object containing the bed file information.
bamFile	Character indicating the alignment and index bam files full path.
fastaFile	Character indicating the full path to the genome reference and index files.
scanBamP	ScanBamParam indicating the parameters the BAM file read.
pileupP	PileupParam indicating the parameters for the pileup build.
BPPARAM	An optional BiocParallelParam instance defining the parallel back-end to be used during evaluation.

Value

data.frame object.

Author(s)

Gabriela A. Merino [e-mail], Cristobal Fresno [e-mail], Yanina Murua [e-mail], Andrea S. Llera [e-mail] and Elmer A. Fernandez [e-mail]

References

1. Morgan M, Pages H, Obenchain V and Hayden N. Rsamtools: Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import. R package version 1.20.1

See Also

Rsamtools-pileup

Examples

##Obtain the pileup matrix for the first amplicon
data(ampliPanel, package="TarSeqQC")
bed<-getBedFile(ampliPanel)[1]
## Defining bam file and fasta file names and paths
bamFile<-system.file("extdata", "mybam.bam", package="TarSeqQC", mustWork=TRUE)
fastaFile<-system.file("extdata", "myfasta.fa", package="TarSeqQC",
    mustWork=TRUE)
## extracting the pileup matrix
myCounts<-pileupCounts(bed, bamFile, fastaFile)
head(myCounts)

gamerino/TarSeqQC documentation built on Feb. 3, 2020, 9:19 p.m.