writeInputsFindhap | R Documentation |
Write inputs into files formatted for findhap
writeInputsFindhap(
opt.file,
X = NULL,
genos.file,
chips = NULL,
snp.coords = NULL,
snp.info.file,
vcf.file = NULL,
yieldSize = 10000,
ped = NULL,
ped.file = NULL,
iters = 4,
Xchrom = 0,
maxlen = 1000,
minlen = 100,
steps = 3,
maxhap = 5000,
hapout = 1,
genout = 1,
damout = 1,
listout = -1,
errate = 0.003,
verbose = 1
)
opt.file |
path to the options file in which findhap's configuration will be saved |
X |
matrix of bi-allelic SNP genotypes encoded in number of copies of the 2nd allele, i.e. as allele doses in 0,1,2, with genotypes in rows and SNPs in columns; missing values should be encoded as NA; if not NULL, will be used in priority even if |
genos.file |
path to the file in which genotypes will be saved |
chips |
if several microarrays were used, provide a vector with chip numbers which names are genotype identifiers (same as in |
snp.coords |
data.frame with SNP identifiers as row names, and two compulsory columns in that order, chromosome identifiers and coordinate/position identifiers; chromosome identifiers should be numeric; other optional column(s) contain the SNP order on the microarray(s) (maximum 10); compulsory if |
snp.info.file |
path to the file in which SNP information will be saved |
vcf.file |
path to the VCF file (if the bgzip index doesn't exist in the same directory, it will be created); used only if |
yieldSize |
number of records to yield each time the file is read from (see |
ped |
data frame of pedigree with four columns in that order, genotype identifiers (same as in |
ped.file |
path to the file in which the pedigree will be saved |
iters |
maximum iterations for haplotype imputation |
Xchrom |
final chromosome number for X, or 0 if no X |
maxlen |
maximum length of segments to check when haplotyping |
minlen |
minimum length of segments to check when haplotyping |
steps |
number of steps to get from maxlen to minlen |
maxhap |
maximum different haplotypes within any segment |
hapout |
output full haplotypes or not |
genout |
output filled genotypes or not |
damout |
output imputed genotypes of parents or not |
listout |
output haplotypes list or not |
errate |
fraction of miscalled genotypes allowed when matching |
verbose |
verbosity level (0/1) |
nothing
Timothee Flutre
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