create_crimap_input: create_crimap_input: Create a CriMAP input file.

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

Description

create_crimap_input: Create a CriMAP input file.

Usage

create_crimap_input(gwaa.data, familyPedigree, analysisID,
  snplist = NULL, chr = NULL, is.X = FALSE, is.Z = FALSE,
  pseudoautoSNPs = NULL, use.mnd = FALSE, use.specific.mnd = NULL,
  outdir = NULL, verbose = TRUE, clear.existing.analysisID = TRUE,
  dummy.mother.id = NULL, dummy.father.id = NULL)

Arguments

gwaa.data	GenABEL gwaa.data object containing genomic data
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.
analysisID	string. Used as an identifier for the chromosome. Must begin with a numeric character as per crimap convention; for example, analysisID = "1a" will output the file "chr1a.gen".
snplist	vector, optional. A list of ordered SNPs. UNless build is run, SNPs will be assumed to be in this order.
chr	string. Chromosome ID if whole chromosome is to be run.
is.X	logical. If true, then all heterozygotes are scored as missing in males, except for pseudoautosomal SNPs when defined (see below)
is.Z	logical. If true, then all heterozygotes are scored as missing in females, except for pseudoautosomal SNPs when defined (see below)
pseudoautoSNPs	Character vector of pseudoautosomal SNP IDs. Only used if is.X or is.Z == TRUE.
use.mnd	logical, default = FALSE. Masks parent offspring genotype mismatches based on output from parse_mend_err
use.specific.mnd	string, path to specific .mnd file to use.
outdir	String, optional. Specify the path of the directory in which the output file should be written.
verbose	Logical. FALSE will suppress messages.
clear.existing.analysisID	Logical, default is TRUE. Overwrites .gen file and deletes crimap files that have the analysisID in the target directory.
dummy.parent.id	numeric. This is an identifier for IDs that should be filled in with blank genotypes, for example, because CRIMAP cannot deal with a single parent.

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