writeInputsFindhap: Write inputs for findhap
In timflutre/rutilstimflutre: Timothee Flutre's personal R code

writeInputsFindhap

R Documentation

Write inputs for findhap

Description

Write inputs into files formatted for findhap

Usage

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
)

Arguments

`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 `vcf.file` is not NULL
`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 `X`)
`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 `X` is specified
`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 `X=NULL`
`yieldSize`	number of records to yield each time the file is read from (see `?TabixFile`)
`ped`	data frame of pedigree with four columns in that order, genotype identifiers (same as in `X`), parent1 identifiers (considered as father/sire), parent2 identifiers (considered as mother/dam), and sex (as M or F)
`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)