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Improved handling of FASTA data (#24)

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Waldir Leoncio 2024-08-09 14:57:07 +02:00
parent 73b0a70138
commit ca358ff0fb
1 changed files with 3 additions and 3 deletions
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6
R/greedyMix.R
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@ -28,8 +28,8 @@ greedyMix <- function(
) { ) {
# Importing and handling data ================================================ # Importing and handling data ================================================
if (tolower(format) %in% "fasta") { if (tolower(format) %in% "fasta") {
data <- load_fasta(data) data <- convert_FASTA_to_BAPS(data)
data <- handleData(data, "FASTA") format <- "baps"
} }
if (tolower(format) %in% "baps") { if (tolower(format) %in% "baps") {
data <- process_BAPS_data(data, NULL) data <- process_BAPS_data(data, NULL)
@ -68,7 +68,7 @@ greedyMix <- function(
# Generating partition summary =============================================== # Generating partition summary ===============================================
ekat <- seq(1L, ninds * c[["rowsFromInd"]], c[["rowsFromInd"]]) ekat <- seq(1L, ninds * c[["rowsFromInd"]], c[["rowsFromInd"]])
c[["rows"]] <- cbind(ekat, ekat + c[["rowsFromInd"]] - 1L) c[["rows"]] <- cbind(ekat, ekat + c[["rowsFromInd"]] - 1L)
logml_npops_partitionSummary <- indMixWrapper(c, npops, counts, sumcounts, max_iter, fixedK, verbose) logml_npops_partitionSummary <- indMixWrapper(c, npops, counts, sumcounts, max_iter, fixedK, verbose) # FIXME: not working for FASTA data
logml <- logml_npops_partitionSummary[["logml"]] logml <- logml_npops_partitionSummary[["logml"]]
npops <- logml_npops_partitionSummary[["npops"]] npops <- logml_npops_partitionSummary[["npops"]]
partitionSummary <- logml_npops_partitionSummary[["partitionSummary"]] partitionSummary <- logml_npops_partitionSummary[["partitionSummary"]]