Whop_readVCF: Reading tabixed VCF files (an interface to WhopGenome)
In PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses

Description Usage Arguments Details Value Examples

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

1 2	Whop_readVCF(v, numcols, tid, frompos, topos, samplenames=NA, gffpath = FALSE, include.unknown=FALSE)

`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

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") !

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

# require(WhopGenome)
# vcf_handle   <- vcf_open("chr2.vcf.gz")
# GENOME.class <- Whop_readVCF(vcf_handle, 1000, "2", 1, 100000)
# GENOME.class
# GENOME.class@region.names

PopGenome documentation built on Feb. 1, 2020, 1:07 a.m.