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Improved handling of supported formats for greedyMix() (#25)

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Waldir Leoncio 2023-09-11 12:37:25 +02:00
parent 76828387a3
commit 3e4044bcec
1 changed files with 8 additions and 6 deletions
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14
R/handleData.R
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@ -21,13 +21,15 @@ handleData <- function(raw_data, format = "Genepop") {
# koodi pienimm?ksi koodiksi, joka isompi kuin mik??n k?yt?ss?oleva koodi. # koodi pienimm?ksi koodiksi, joka isompi kuin mik??n k?yt?ss?oleva koodi.
# T?m?n j?lkeen funktio muuttaa alleelikoodit siten, ett?yhden lokuksen j # T?m?n j?lkeen funktio muuttaa alleelikoodit siten, ett?yhden lokuksen j
# koodit saavat arvoja v?lill?1,...,noalle(j). # koodit saavat arvoja v?lill?1,...,noalle(j).
nloci <- switch(
tolower(format),
"genepop" = ncol(raw_data) - 1L,
"baps" = ncol(raw_data) - 1L,
"fasta" = ncol(raw_data),
"vcf" = stop("VCF format not supported for processing yet"),
"bam" = stop("BAM format not supported for processing yet")
)
data <- as.matrix(raw_data) data <- as.matrix(raw_data)
if (format %in% c("genepop", "baps")) {
nloci <- size(raw_data, 2) - 1
} else {
nloci <- size(raw_data, 2)
}
dataApu <- data[, 1:nloci] dataApu <- data[, 1:nloci]
nollat <- matlab2r::find(dataApu == 0) nollat <- matlab2r::find(dataApu == 0)
if (!isempty(nollat)) { if (!isempty(nollat)) {