extracts SNP annotation from IMPUTE files...

extract.annotation.impute {GenABEL}R Documentation

extracts SNP annotation from IMPUTE files...

Description

extracts SNP annotation from IMPUTE files

Usage

extract.annotation.impute(genofile, infofile, chromosome=NA,
    order_geno_snp_a0_a1=c(2, 4:5), skip_geno=0,
    order_info_snp_pos_freq1_info_qual_type=c(2:7), skip_info=1,
    allow_duplicated_names=FALSE)

Arguments

genofile IMPUTE genotype file name
infofile IMPUTE info-file name
chromosome chromosome
order_geno_snp_a0_a1 which columns to extract from geno-file, and what is the order for snp name, a0, and a0? (default is OK)
skip_geno how many lines of geno-file are to be skept? (default is OK)
order_info_snp_pos_freq1_info_qual_type which columns to extract from info-file, and what is the order for SNP name, position, frequency of allele 1, info (Rsq), and quality (average max post prob)? Dafult works for IMPUTE v2.0, but has to be changed for other versions. Always check!
skip_info how many lines of info-file are to be skept before information starts? IMPUTE v2.0 has a header line, therefore skip_info=1 works fine; this may be different for other versions of IMPUTE
allow_duplicated_names if duplicated SNP names are allowed (same order in geno and info- files is assumed then)

Details

This function extracts SNP annotation information from IMPUTE files. The major problem at the moment that info-file format of IMPUTE is a little bit unstable (reported information and column order varies between impute v1, v2, and beta-version). Therefore take special care to read specification of 'order_info_snp_pos_freq1_info_qual_type'

Value

data frame containing annotaton

Author(s)

Yurii Aulchenko


[Package GenABEL version 1.6-7 Index]