Whop_readVCF: Reading tabixed VCF files (an interface to WhopGenome)

Description Usage Arguments Details Value Examples

Description

This function provides an interface to the WhopGenome package which is specialized to read tabix-indexed VCF files.

Usage

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Whop_readVCF(v, numcols, tid, frompos, topos,
        samplenames=NA, gffpath = FALSE, include.unknown=FALSE)

Arguments

v

a vcf_handle returned from vcf_open()

numcols

number of SNPs that should be read in as one chunk

tid

which chromosome ? (character)

frompos

start of the region

topos

end of the region

samplenames

a vector of individual names/IDs

gffpath

the corresponding GFF file

include.unknown

including positions with unknown nucleotides

Details

WhopGenome is required ! require(WhopGenome) WhopGenome provides some powerful filter meachanisms which can be applied to the VCF reading process. The filter rules can be set via WhopGenome functions. Whop_readVCF expects a vcf_handle returned from vcf_open. The Whop_readVCF function expects a tabixed VCF with a diploid GT-field.
In case of haploid data, the GT-field has to be transformed to a pseudo- diploid field (0 -> 0|0 etc.). An alternative is to use readData(..., format="VCFhap") which can read non-tabixed haploid VCFs directly.
The ff-package we use limits the data size to individuals * (number of SNPs) <= .Machine$integer.max
In case of very large data sets, the bigmemory package will be used.
This may slow down calculations.
See also readData(..., format="VCF") !

Value

The function creates an object of class "GENOME"

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The following slots will be filled in the "GENOME" object
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Slot Description
1. n.sites total number of sites
2. n.biallelic.sites number of biallelic sites
3. region.data some detailed information on the data read
4. region.names names of regions

Examples

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# require(WhopGenome)
# vcf_handle   <- vcf_open("chr2.vcf.gz")
# GENOME.class <- Whop_readVCF(vcf_handle, 1000, "2", 1, 100000)
# GENOME.class
# [email protected]

pievos101/PopGenome documentation built on May 16, 2019, 2:54 a.m.