readPileup {Rsamtools} | R Documentation |
Import samtools 'pileup' files.
Description
Import files created by evaluation of samtools' pileup -cv
command.
Usage
readPileup(file, ...)
## S4 method for signature 'connection'
readPileup(file, ..., variant=c("SNP", "indel", "all"))
Arguments
file |
The file name, or
|
... |
Additional arguments, passed to methods. For instance,
specify |
variant |
Type of variant to parse; select one. |
Value
readPileup
returns a GRanges
object.
The value returned by variant="SNP"
or variant="all"
contains:
- space:
The chromosome names (fastq ids) of the reference sequence
- position:
The nucleotide position (base 1) of the variant.
- referenceBase:
The nucleotide in the reference sequence.
- consensusBase;
The consensus nucleotide, as determined by samtools pileup.
- consensusQuality:
The phred-scaled consensus quality.
- snpQuality:
The phred-scaled SNP quality (probability of the consensus being identical to the reference).
- maxMappingQuality:
The root mean square mapping quality of reads overlapping the site.
- coverage:
The number of reads covering the site.
The value returned by variant="indel"
contains space, position,
reference, consensus, consensusQuality, snpQuality, maxMappingQuality,
and coverage fields, and:
- alleleOne, alleleTwo
The first (typically, in the reference sequence) and second allelic variants.
- alleleOneSupport, alleleTwoSupport
The number of reads supporting each allele.
- additionalIndels
The number of additional indels present.
Author(s)
Sean Davis
References
http://samtools.sourceforge.net/
Examples
fl <- system.file("extdata", "pileup.txt", package="Rsamtools",
mustWork=TRUE)
(res <- readPileup(fl))
xtabs(~referenceBase + consensusBase, mcols(res))[DNA_BASES,]
## Not run: ## uses a pipe, and arguments passed to read.table
## three successive piles of 100 records each
cmd <- "samtools pileup -cvf human_b36_female.fa.gz na19240_3M.bam"
p <- pipe(cmd, "r")
snp <- readPileup(p, nrow=100) # variant="SNP"
indel <- readPileup(p, nrow=100, variant="indel")
all <- readPileup(p, nrow=100, variant="all")
## End(Not run)