readGenoVCF: Read genotype data from a VCF file.

In gact/shmootl: QTL Analysis Utilities for Yeast

Description

This function reads SNP genotype data from one or more VCF files, and returns these as an R/qtl cross geno object.

Usage

readGenoVCF(..., samples, founders = NULL, alleles = NULL)

Arguments

...	Input VCF file paths.
samples	Cross sample IDs.
founders	Founder sample IDs.
alleles	Mapping of founder sample IDs to founder allele symbols.

Details

If no founder samples are specified, this function assigns enumerated genotypes at each locus according to the observed raw SNP genotype. So for example, if the raw SNP alleles at a given locus are 'A' and 'C', samples are assigned the genotypes '1' and '2', respectively.

If founder samples are specified, this function assigns to each marker a genotype symbol consisting of alleles that each correspond to a specific founder.

If the alleles parameter is specified, this must be a mapping of founder sample IDs to allele symbols (e.g. mapping( c(DBVPG6044 = 'W', Y12 = 'S') )). If the alleles parameter is not specified, allele symbols are taken from the letters of the alphabet (i.e. 'A', 'B' etc.).

Value

An R/qtl cross geno object.

Raw Alleles and Genotypes

A raw allele is the original marker value. Single-nucleotide variants (i.e. 'A', 'C', 'G', or 'T') are commonly used, and are the only kind of marker supported by the shmootl package. These must be converted into another kind of allele before doing QTL analysis.

For a given ploidy N, a raw genotype is the concatenation of the set of N raw alleles. For example, given two 'A' alleles at a homozygous diploid marker, the genotype is 'AA'.

Enumerated Alleles/Genotypes

An enumerated allele/genotype is a number representing the order of occurrence of raw or founder genotypes at a specific marker (e.g. '1' for the first observed allele, '2' for the second). Enumerated alleles and genotypes are identical, regardless of ploidy. The process of enumerating genotypes is done independently for each marker, so a given enumerated genotype does not have the same meaning across markers.

Founder Alleles and Genotypes

A founder allele is a single letter corresponding to a specific founder strain, indicating that the region containing the marker derives from that founder. For example, 'W' might be used to represent the Western Africa founder strain DBVPG6044, or 'S' might be used for the Sake strain Y12).

For a given ploidy N, a founder genotype is the concatenation of the set of N founder alleles. For example, given one founder allele 'W' and another 'S', the founder genotype is 'WS'.

See Also

Other VCF functions: getSamplesVCF

gact/shmootl documentation built on Nov. 11, 2021, 6:23 p.m.