get.variants: get.variants

In dmgatti/DOQTL: Genotyping and QTL Mapping in DO Mice

get.variants

Description

Get SNPs for a set of strains for a specific regions of chromosomes.

Usage

  get.variants(file = "ftp://ftp.jax.org/SNPtools/variants/cc.snps.NCBI38.txt.gz", 
  chr, start, end, type = c("snp", "indel", "sv"), strains, polymorphic  =  TRUE, 
  quality)

Arguments

file	Character, full path to the SNP file to use. Default is the file at the Center for Genome Dynamics at The Jackson Laboratory.
chr	Numeric vector, chr for each start and end position. Chr, start and end must all have the same length.
start	Numeric vector, start position in Mb or bp for each chr. Chr, start and end must all have the same length.
end	Numeric vector, end position in Mb or bp for each chr. Must be greater than or equal to the corresponding start value. Chr, start and end must all have the same length.
type	Character, with one of "snp", "indel", "sv". Indicates the type of variantes being queried.
strains	Character vector, listing the strains to retrieve. The names can be obtained from get.strains(). Default returns all strains.
polymorphic	Boolean. Default = TRUE. If TRUE, retrieve only SNPs that are polymorphic among the requested strains. If FALSEALSE, return all SNPs in the requested interval(s).
quality	Integer, denoting the confidence levels to return. This looks at the quality column of all requested strains and takes values greater than or equal to the given number. Look at the documentation for the SNP file you are using for details on the quality score. Default returns all SNPs.

Value

A list of data.frames for each region requested. Each data.frame will contain five header columns; ID, CHROM, POS, REFALSE & ALT corresponding to the SNP ID, chromosome, bp position, reference and alternate alleles. There follows two columns for each requested strain containing the allele calls and quality scores for each strain. If there is only one requested region, a single data frame is returned.

Author(s)

Daniel Gatti

See Also

get.strains

Examples

  ## Not run: 
  available.strains = get.strains()
  strains = available.strains[c(2, 5, 8, 9, 13:15, 17)]
  snps = get.variants(chr = 7, start = 103, end = 105, strains = strains)
  
## End(Not run)

dmgatti/DOQTL documentation built on April 7, 2024, 10:35 p.m.