R: extracts SNP annotation from IMPUTE files

extract.annotation.impute {GenABEL} | R Documentation

## extracts SNP annotation from IMPUTE files

### Description

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'

### 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)

### Value

data frame containing annotaton

### Author(s)

Yurii Aulchenko

[Package GenABEL version 1.8-0 Index]