export.doqtl: Export genotyping result in format suitable for DOQTL

In andrewparkermorgan/argyle: Basic interface and QC for genotypes from Illumina Infinium arrays

Description

Export genotyping result in format suitable for DOQTL

Usage

export.doqtl(gty, where = "doqtl.Rdata", recode = FALSE, ...)

Arguments

gty	a genotypes object with intensity data attached
where	name of output file, including path (else it goes in working directory)
recode	if TRUE, genotype calls will be recoded 0/1/2 with respect to reference alleles before the genotypes matrix is saved
...	ignored

Value

Returns TRUE on completion. The Rdata file at where contains the following objects:

G – genotype calls matrix x – matrix of x-intensities y – matrix of y-intensities sex – named vector of sample sexes (NA if missing) snps – the marker map attached to the input object All matrices are sites x samples, following the convention of this pacakge, and have both row and column names.

References

DOQTL home: http://cgd.jax.org/apps/doqtl/DOQTL.shtml

Gatti DM et al. (2014) Quantitative trait locus mapping methods for Diversity Outbred mice. G3 4(9): 1623-1633. doi:10.1534/g3.114.013748.

Svenson KL et al. (2012) High-resolution genetic mapping using the mouse Diversity Outbred population. Genetics 190(2): 437-447. doi:10.1534/genetics.111.132597.

andrewparkermorgan/argyle documentation built on May 10, 2019, 11:08 a.m.