snpinfo_to_map {qtl2pattern}

Convert SNP info to map

Description

Convert SNP info to map

Usage

snpinfo_to_map(snpinfo)

Arguments

snpinfo

Data frame with SNP information with the following columns (the last three are generally derived from with index_snps):

• chr - Character string or factor with chromosome

• pos - Position (in same units as in the "map" attribute in genoprobs.

• sdp - Strain distribution pattern: an integer, between 1 and 2^n - 2 where n is the number of strains, whose binary encoding indicates the founder genotypes

• snp - Character string with SNP identifier (if missing, the rownames are used).

• index - Indices that indicate equivalent groups of SNPs.

• intervals - Indexes that indicate which marker intervals the SNPs reside.

• on_map - Indicate whether SNP coincides with a marker in the genoprobs

Value

map as list of vectors of marker positions.