read.snpdata.impute: Read genotype dosages in the format output by IMPUTE.
Description
Reads sample information and genotype data from paired sample and
genotype files, as generated by the IMPUTE and IMPUTE2 genotype
imputation programs and as used by the SNPTEST program. Returns the
data in a standard format (see snpdata) that can be used by
other functions in this package.
filename for genotypes, assumed IMPUTE verbose format.
phenotypes
if not null, a data frame of phenotypes to be merged with the
genotypes; first two columns will be used to match against first two
columns of the samplefile.
Value
Returns a list with snpinfo and data slots, see snpdata.
Details
The sample file is assumed to have two header lines, of which the first
header line is assumed to be column names and the second header line
is assumed to be the “000Ps” line. The genotype file is
assumed to have one line for each SNP, of which the first five columns
contain information about the SNP, followed by triplets of numeric
values giving the probabilities of genotypes 0, 1, 2, for each sample
in turn.
This function will be slow for large input files. Best to use gtool
or grep/awk out the relevant lines (SNPs) into a smaller file first.