From ca358ff0fbf635af8515118996c7ea9d73fc478c Mon Sep 17 00:00:00 2001 From: Waldir Leoncio Date: Fri, 9 Aug 2024 14:57:07 +0200 Subject: [PATCH] Improved handling of FASTA data (#24) --- R/greedyMix.R | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/R/greedyMix.R b/R/greedyMix.R index 305ca25..dd0d117 100644 --- a/R/greedyMix.R +++ b/R/greedyMix.R @@ -28,8 +28,8 @@ greedyMix <- function( ) { # Importing and handling data ================================================ if (tolower(format) %in% "fasta") { - data <- load_fasta(data) - data <- handleData(data, "FASTA") + data <- convert_FASTA_to_BAPS(data) + format <- "baps" } if (tolower(format) %in% "baps") { data <- process_BAPS_data(data, NULL) @@ -68,7 +68,7 @@ greedyMix <- function( # Generating partition summary =============================================== ekat <- seq(1L, ninds * c[["rowsFromInd"]], c[["rowsFromInd"]]) 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"]] npops <- logml_npops_partitionSummary[["npops"]] partitionSummary <- logml_npops_partitionSummary[["partitionSummary"]]