#' Input tools
#'
#' \code{create_all_inputs}
#'
#' @param refpop1_integer a haplotype matrix.
#' @param refpop2_integer a haplotype matrix.
#' @param refpop1 a haplotype matrix.
#' @param refpop2 a haplotype matrix.
#' @param H.integer a haplotype matrix.
#' @param H a haplotype matrix.
#' @param true.ancestry.matrix a matrix.
#' @param directory a character string.
#' @param pos_map a numeric vector.
#' @param gen_map a numeric vector.
#' @param chr an integer.
#' @param ref a numeric vector.
#' @param alt a numeric vector.
#' @param pop a numeric vector.
#' @param parameters a data.frame.
#' @param gt.df a data.frame.
#'
#' @return
#'
#' @export
#'
create_all_inputs = function(refpop1_integer,
refpop2_integer,
refpop1,
refpop2,
H.integer,
H,
true.ancestry.matrix,
directory,
pos_map,
gen_map,
chr,
ref,
alt,
pop,
parameters,
gt.df){
### pcadapt ###
input.pcadapt <- create_input_pcadapt(H1 = refpop1_integer,
H2 = refpop2_integer,
Hadm = H.integer)
write.table(input.pcadapt,
paste0(directory, "/simu.pcadapt"),
col.names = FALSE,
row.names = FALSE,
quote = FALSE)
### RFMix ###
create_input_RFMix(H1 = refpop1_integer,
H2 = refpop2_integer,
Hadm = H.integer,
genetic.map = gen_map,
RFMix.output = paste0(directory, "/RFMix"))
### loter ###
create_input_loter(H1 = H1.integer,
H2 = H2.integer,
Hadm = H.integer,
paste0(dir.name, "/"))
### Hapmix ###
create_input_Hapmix(H1 = H1.integer,
H2 = H2.integer,
Gadm = haplo_to_geno(H.integer),
gen_map = gen_map,
phys_map = pos_map,
chr = chr,
Hapmix.output = directory)
write.table(pop,
paste0(directory, "/pop.txt"),
col.names = FALSE,
row.names = FALSE,
quote = FALSE)
write.table(parameters,
paste0(directory, "/parameters.txt"),
col.names = TRUE,
row.names = FALSE,
quote = FALSE)
write.table(gt.df$gt.df,
paste0(directory, "/gt.txt"),
col.names = TRUE,
row.names = FALSE,
quote = FALSE)
write.table(true.ancestry.matrix,
paste0(directory, "/adm_true_ancestry.txt"),
col.names = FALSE,
row.names = FALSE,
quote = FALSE)
write.table(H,
paste0(directory, "/admpop.phased"),
col.names = FALSE,
row.names = FALSE,
quote = FALSE)
}
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