snpStats (version 1.18.0)

read.impute: Read genotypes imputed by the IMPUTE2 program

Description

The IMPUTE2 program generates, for each SNP and each subject, posterior probabilities for the three genotypes. This function reads such data as a SnpMatrix object, storing the posterior probabilities to as much accuracy allowed by a one-byte coding

Usage

read.impute(file, rownames = NULL, nsnp = NULL, snpcol = 2)

Arguments

file

The input file name. This file my be gzipped.

rownames

The row names for the output object. Note that these correspond to groups of three columns in the input file. If not supplied, names are generated as Sample1, Sample2 etc.

nsnp

The number of SNPs to be read in. This corresponds with the number of lines in the input file. If not supplied, the function does a preliminary pass to determine the number of lines

snpcol

Which column of the input will be used as the SNP name. Default is column 2

Value

an object of class SnpMatrix

Details

No provision is made for data for the X chromosome. Such data must be first read as a SnpMatrix and subsequently coerced to an XSnpMatrix object

See Also

SnpMatrix-class

Examples

##---- No example available yet