rehh (version 2.0.1)

data2haplohh: Converting data into an object of class haplohh

Description

Converts input file data into an object of class haplohh.

Usage

data2haplohh(hap_file,map_file,min_maf=0,min_perc_geno.hap=100,
min_perc_geno.snp=100,chr.name=NA,popsel=NA,recode.allele=FALSE,
haplotype.in.columns=FALSE)

Arguments

hap_file

Path to the file containing haplotype data (see details section below for information about input file format)

map_file

Path to the file containing map information (see details section below for information about input file format

min_maf

Threshold on Minor Allele Frequency (SNPs displaying a MAF lower than min_maf are discarded)

min_perc_geno.hap

Threshold on percentage of missing data for haplotypes (Haplotypes with less than min_perc_geno.hap percent SNPs genotyped are discarded). By default, min_perc_geno.hap=100, hence only fully genotyped haplotypes are retained

min_perc_geno.snp

Threshold on percentage of missing data for SNPs (SNPs genotyped on less than min_perc_geno.snp percent haplotypes are discarded). By default, min_perc_geno.snp=100, hence only fully genotyped SNPs are retained

chr.name

Name of the chromosome considered (relevant if several chromosomes are represented in the map file)

popsel

Code of the population considered in the fastPHASE output haplotype file (relevant if hap_file is a fastPHASE output and haplotypes originate from different population)

recode.allele

If TRUE, allele in the haplotypes are recoded according to the map file information. If FALSE a rough verification is performed to check only 0 (code for missing data), 1 (code for ancestral allele) or 2 (code for derived allele) are present in the haplotype file

haplotype.in.columns

If TRUE, phased input haplotypes are assumed to be in columns (as produced by the SHAPEIT2 program (O'Connell et al., 2014).

Value

Details

Three haplotype input formats are supported: i) a standard format with haplotype in row and snps in column (with no header and a haplotype id); ii) a (transposed) format similar to the one produced by the phasing program SHAPEIT2 program (O'Connell et al., 2014) in which haplotypes are in columns and snps in rows (with no header and no snp id); and iii) output files from fastPHASE program (Sheet and Stephens, 2006). If the input haplotypes are not in transposed format (i.e., haplotype.in.columns is FALSE, as by default), the function automatically checks if the file is in fastPHASE output format. In this latter case, if haplotypes originate from several different population were phased simultaneously (-u fastPHASE option was used), the function ask interactively which population should be considered (a list of population number are proposed) unless specified with the popsel argument. Map file contains SNPs information in five columns SNP names, chromosome, position, ancestral and derived allele. SNPs must be in the same order as in the haplotype for the chromosome considered. If several chromosomes are represented in the map file, one can provide the name of the chromosome of interest (corresponding to the haplotype under study) with chr.name argument. Haplotype are recoded (if recode.allele option is activated) according to the ancestral and derived allele definition available in the map file (fourth and fifth columns) as :0=missing data, 1=ancestral allele, 2=derived allele. If such a coding is detected, no recoding is performed. Note that Rsb statistics does not consider ancestral and derived allele status information. Finally, the arguments min\_perc\_geno.hap, min\_perc\_geno.snp and min\_maf are evaluated in this order.

References

Scheet P, Stephens M (2006) A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase. Am J Hum Genet, 78, 629-644. O'Connell J, Gurdasani D, Delaneau O, et al (2014) A general approach for haplotype phasing across the full spectrum of relatedness. PLoS Genet, 10, e1004234.

See Also

calc_ehh,calc_ehhs,scan_hh,make.example.files

Examples

#Copy example files in the current working directory.
make.example.files()
#using the fastPHASE output haplotype example file
hap<-data2haplohh(hap_file="bta12_hapguess_switch.out",map_file="map.inp",
min_maf=0.05,popsel=7,chr.name=12,recode.allele=TRUE)
#using the standard output haplotype example file
hap<-data2haplohh(hap_file="bta12_cgu.hap",map_file="map.inp",
min_maf=0.05,chr.name=12,recode.allele=TRUE)