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# smartsnp v.1
# Coding start date = 26/01/2021
# smartsnp::read_packedancestrymap by Robert Maier (rmaier@broadinstitute.org), modified by Christian D. Huber (christian.domitian.huber@gmail.com)
# Loading genotype data that is in packedancestrymap format standing for binary or compressed data
#' @name read_packedancestrymap
#'
#' @title Read Files in PACKEDANCESTRYMAP format
#'
#' @description This function loads genotype data in \code{PACKEDANCESTRYMAP} format (binary or compressed).
#'
#' @param pref The prefix of the file name that contains the genotype data (i.e., without the \code{*.geno}).
#' @return Returns a list containing a single element:
#' \itemize{
#' \item {\code{geno}} {Genotype data as R matrix.}\cr
#' }
#'
#' @export
read_packedancestrymap = function (pref)
{
pref = normalizePath(pref, mustWork = FALSE)
fl = paste0(pref, ".geno")
conn = file(fl, "rb")
hd = strsplit(readBin(conn, "character", n = 1), " +")[[1]]
close(conn)
nindall = as.numeric(hd[2])
nsnpall = as.numeric(hd[3])
message(basename(pref), ".geno has ", nindall,
" samples and ", nsnpall, " SNPs.")
message("Reading data for ", nindall, " samples and ",
nsnpall, " SNPs")
message("Expected size of genotype data: ",
round((nsnpall * nindall * 8 + nsnpall * 112)/1e+06), " MB")
indvec = rep(1, nindall)
geno = cpp_read_packedancestrymap(fl, nsnpall, nindall, indvec,
first = 0, last = nsnpall, transpose = FALSE,
verbose = FALSE)
outlist = list(geno = geno)
outlist
}
##### smartsnp v.1
##### Coding end date = 08/02/2021
##### smartsnp::read_packedancestrymap spelling checked by Salvador Herrando-Perez (salherra@gmail.com)
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