get_snp_probs: Get the SNP probs nearest to the given chr and position.

In dmgatti/qtl2med: Mediation Analysis for qtl2

Description

chr: character indicating the chromosome to use. This must match one of the names of genoprobs and map. pos: numeric value in Mb indicating the position on the chromosome. genoprobs: list containing 3-dimensional arrays of allele probs, one for each chromosome. In qtl2 format. Samples in rows, 8 founders in columns, markers in slices. map: list containing numeric vectors of marker positions in Mb. query_fxn: function for querying the CC_SNP data base. Obtain this

Usage

get_snp_probs(chr, pos, genoprobs, map, query_fxn)

Value

an n x 1 numeric matrix.

Examples

query_fxn = create_variant_query_func(cc_dbfile, filter = "type=='snp'")
get_snp_probs = function(chr = "1", pos = 5.0, genoprobs = genoprobs, map = map, query_fxn = query_fxn)

dmgatti/qtl2med documentation built on May 8, 2019, 11:55 p.m.