parse_mend_err: parse_mend_err: Parse output from CriMAP .loc files

In susjoh/crimaptools: Tools for preparing files and parsing output for the programme Cri-MAP

Description

parse_mend_err: Parse output from CriMAP .loc files

Usage

parse_mend_err(prefile, genfile, save.mendfile = TRUE, familyPedigree,
  is.X = FALSE, is.Z = FALSE, pseudoautoSNPs = NULL,
  genabel.phdata = NULL)

Arguments

prefile	.pre file (output from prepare function)
genfile	.gen file
save.mendfile	logical. Default = TRUE, saves .mnd file
familyPedigree	data.frame containing columns ANIMAL, FATHER, MOTHER and FAMILY. FAMILY defines family groups for crimap. IDs in ANIMAL can be repeated within and between families if necessary.
is.X	logical. If true, then Mendelian errors are dealt with differently for the homogametic sex (see below).
is.Z	logical. If true, then Mendelian errors are dealt with differently for the homogametic sex (see below).
pseudoautoSNPs	Character vector of pseudoautosomal SNP IDs. Only used if is.X or is.Z == TRUE.
genabel.phdata	GenABEL phdata object, or data frame with fields information on "id" and sex"

susjoh/crimaptools documentation built on Oct. 13, 2020, 3:24 p.m.