pileupAsGRanges: Summarize reads for certain region

In lawremi/biovizBase: Basic graphic utilities for visualization of genomic data.

Description

This function summarize reads from bam files for nucleotides on single base unit in a given region, this allows the downstream mismatch summary analysis.

Usage

pileupAsGRanges(bams, regions, DNABases=c("A", "C", "G", "T", "N"), ...)

Arguments

bams	A character which specify the bam file path.
regions	A GRanges object specifying the region to be summarized. This passed to which arguments in ApplyPileupsParam.
DNABases	Nucleotide type you want to summarize in the result and in specified order. It must be one or more of A,C,G,T,N.
...	Extra parameters passed to ApplyPileupsParam.

Details

It's a wrapper around applyPileup function in Rsamtools package, more detailed control could be found under manual of ApplyPileupsParam function in Rsamtools. pileupAsGRanges function return a GRanges object which including summary of nucleotides, depth, bam file path. This object could be read directly into pileupGRangesAsVariantTable function for mismatch summary.

Value

A GRanges object, each row is one single base unit. and elementMetadata contains summary about this position about all nucleotides specified by DNABases. and depth for total reads, bam for file path.

Author(s)

Michael Lawrence, Tengfei Yin

Examples

## Not run: 
library(Rsamtools)
data(genesymbol)
library(BSgenome.Hsapiens.UCSC.hg19)    
bamfile <- system.file("extdata", "SRR027894subRBM17.bam", package="biovizBase")
test <- pileupAsGRanges(bamfile, region = genesymbol["RBM17"])
test.match <- pileupGRangesAsVariantTable(test, Hsapiens)
head(test[,-7])
head(test.match[,-5])

## End(Not run)

lawremi/biovizBase documentation built on Dec. 21, 2021, 9:42 a.m.