pileupAsGRanges {biovizBase} | R Documentation

## Summarize reads for certain region

### 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)

[Package biovizBase version 1.30.1 Index]