writeInputsFastphase | R Documentation |
Use the external software fcGENE from Roshyara and Scholz (2014).
writeInputsFastphase(X, snp.coords, alleles, file, verbose = 0)
X |
matrix of bi-allelic SNP genotypes encoded, for each SNP, in number of copies of its second allele, i.e. as allele doses in 0,1,2, with genotypes in rows and SNPs in columns; the "second" allele is arbitrary, it corresponds to the second column of |
snp.coords |
data.frame with SNP identifiers as row names, and two columns, "chr" and "coord" or "pos" |
alleles |
data.frame with SNPs in rows (names as row names) and alleles in columns (exactly 2 columns are required); the second column should correspond to the allele which number of copies is counted at each SNP in |
file |
write the genotype data to this file (for instance 'genotypes_fastphase.txt' or 'genotypes_fastphase.txt.gz', but don't use |
verbose |
verbosity level (0/1/2) |
nothing
Timothee Flutre
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