writeXtoInp {SNPknock}

Convert genotypes X into the fastPHASE input format

Description

This function converts a genetic matrix X into the fastPHASE input format and saves it to a user-specified file. Then, an HMM can be fitted by calling fastPHASE with runFastPhase.

Usage

writeXtoInp(X, phased = FALSE, out_file = NULL)

Arguments

X

either a matrix of size n-by-p containing unphased genotypes for n individuals, or a matrix of size 2n-by-p containing phased haplotypes for n individuals.

phased

whether the data are phased (default: FALSE). If this is equal to TRUE, each pair of consecutive rows will be assumed to correspond to phased haplotypes from the same individual.

out_file

a string containing the path of the output file onto which X will be written (default: NULL). If this is equal to NULL, a temporary file in the R temporary directory will be used.

Value

A string containing the path of the output file onto which X was written. This is useful to find the data when the default option for 'out_file' is used and X is written onto a temporary file in the R temporary directory.

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. doi: 10.1086/502802.

See Also

Other fastPHASE: loadHMM, runFastPhase

Examples

# Convert unphased genotypes
# Load an example data matrix X from the package installation directory.
X_file = system.file("extdata", "genotypes.RData", package = "SNPknock")
load(X_file)
# Write X in a temporary file
Xinp_file = writeXtoInp(X)

# Convert phased haplotypes
# Load an example data matrix H from the package installation directory.
H_file = system.file("extdata", "haplotypes.RData", package = "SNPknock")
load(H_file)
# Write H in a temporary file
Hinp_file = writeXtoInp(H, phased=TRUE)