writeXtoInp.RdThis 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.
writeXtoInp(X, phased = FALSE, out_file = NULL)
| 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. |
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.
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 .
Other fastPHASE: loadHMM,
runFastPhase
# 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)