writeXtoInp function

Convert genotypes X into the fastPHASE input format

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 .

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.

Returns

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.

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)

References

Rdpack::insert_ref(key="scheet2006",package="SNPknock")

See Also

Other fastPHASE: loadHMM, runFastPhase