writeInputsFimpute: Write inputs for FImpute
In timflutre/rutilstimflutre: Timothee Flutre's personal R code

writeInputsFimpute

R Documentation

Write inputs for FImpute

Description

Write inputs into files formatted for FImpute.

Usage

writeInputsFimpute(
  ctl.file,
  X = NULL,
  genos.file,
  chips = NULL,
  snp.coords = NULL,
  snp.info.file,
  vcf.file = NULL,
  yieldSize = 10000,
  ped = NULL,
  ped.file = NULL,
  title = "FImpute",
  out.dir,
  hap.lib.file = NULL,
  add.ungen = NULL,
  parentage.test = NULL,
  ped.depth = NULL,
  turn.off.fam = FALSE,
  turn.off.pop = FALSE,
  save.partial = FALSE,
  save.genos = FALSE,
  save.hap.lib = FALSE,
  random.fill = FALSE,
  nb.jobs = 1,
  verbose = 1
)

Arguments

`ctl.file`	path to the control file in which FImpute'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; the maximum length of genotypes identifiers is 30 characters; 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; the maximum length of SNP identifiers is 50 characters; 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
`title`	character identifying the analysis
`out.dir`	directory in which the output files will be saved
`hap.lib.file`	path to a file containing a haplotype library
`add.ungen`	to add ungenotyped genotypes in the imputation process, provide a list such as `list(min.fsize=4, output.min.fsize=4, output.min.call.rate=0.9)`
`parentage.test`	check for parentage errors
`ped.depth`	to set a maximum number of generations to be traced for family imputation, provide a number
`turn.off.fam`	turn off family imputation
`turn.off.pop`	turn off population imputation
`save.partial`	save partial calls
`save.genos`	save genotypes instead of haplotypes (encoded as 0,1,2,5/NA)
`save.hap.lib`	save the haplotype library built from reference individuals
`random.fill`	ramdom filling (imputation) based on allele frequency; useful to assess minimum accuracy
`nb.jobs`	number of jobs
`verbose`	verbosity level (0/1)