Read file with information about SNPs chromosome and position, for example from regular PLINK .map OR .bim file

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Description

These files have (at least) the following columns (separated by white space):

  • column 1: chromosome

  • column 2: variant name

  • column 3: genetic distance in morgans (optional, see the morgans option)

  • column 4: base-pair position (bp units)

Usage

1
readMapFile(filename = "NULL", morgans = TRUE)

Arguments

filename

character, path to input file containing genomic map data, e.g. a Plink .map, .bim or .tped file.

morgans

logical, indicate whether input file contains column with genetic distance between SNPs (in which case the bp positions are in the fourth column)

Value

matrix object with columns contains chromosome, rsID and position in bp

Author(s)

Sodbo Sharapov

See Also

read.haplo, read.haplo.pedfile, read.haplo.bedfile, read.haplo.shapeit_haps

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