readMapFile: Read file with information about SNPs chromosome and...

In GreenwoodLab/RVPedigree: Methods for Family-Based Rare-Variant Genetic Association Tests

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

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

GreenwoodLab/RVPedigree documentation built on May 6, 2019, 6:33 p.m.