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Added function to convert from FASTA to BAPS (#24)

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Waldir Leoncio 2024-08-09 13:19:35 +02:00
parent 6e08c35f13
commit 7b7968f00b
5 changed files with 44 additions and 1 deletions
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1
NAMESPACE
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@ -1,5 +1,6 @@
# Generated by roxygen2: do not edit by hand
export(convert_FASTA_to_BAPS)
export(greedyMix)
export(handleData)
export(importFile)

15
R/convert_FASTA_to_BAPS.R Normal file
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@ -0,0 +1,15 @@
#' @title Convert from FASTA to BAPS
#' @description Converts a file (not an R object) from FASTA to BAPS format
#' @param file filename of FASTA file
#' @return `data` in BAPS format
#' @author Waldir Leoncio
#' @export
#' @examples
#' file <- system.file("extdata", "FASTA_clustering_haploid.fasta", package = "rBAPS")
#' convert_FASTA_to_BAPS(file)
convert_FASTA_to_BAPS <- function(file) {
data <- load_fasta(file) # Processing data
data <- cbind(data, seq_len(nrow(data))) # Add IDs of individuals (sequential)
data[data == 0] <- -9 # Because zeros (missing) in BAPS are coded as -9
return(data)
}

3
R/greedyMix.R
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@ -28,7 +28,8 @@ greedyMix <- function(
) {
# Importing and handling data ================================================
if (tolower(format) %in% "fasta") {
stop("FASTA format not yet supported on greedyMix")
data <- load_fasta(data)
data <- handleData(data, "FASTA")
}
if (tolower(format) %in% "baps") {
data <- process_BAPS_data(data, NULL)

2
R/handleData.R
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@ -30,6 +30,7 @@ handleData <- function(raw_data, format = "Genepop") {
"bam" = stop("BAM format not supported for processing yet")
)
data <- as.matrix(raw_data)
dataApu <- data[, seq_len(nloci)]
nollat <- matlab2r::find(dataApu == 0)
if (!isempty(nollat)) {
@ -54,6 +55,7 @@ handleData <- function(raw_data, format = "Genepop") {
alleleCodes[, i] <- as.matrix(c(alleelitLokuksessaI, zeros(puuttuvia, 1)))
}
# This is where data gets converted to {1, 2, 3, 4} for {A, C, G, T}
for (loc in seq_len(nloci)) {
for (all in seq_len(noalle[loc])) {
data[matlab2r::find(data[, loc] == alleleCodes[all, loc]), loc] <- all

24
man/convert_FASTA_to_BAPS.Rd Normal file
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@ -0,0 +1,24 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/convert_FASTA_to_BAPS.R
\name{convert_FASTA_to_BAPS}
\alias{convert_FASTA_to_BAPS}
\title{Convert an R object from FASTA to BAPS format}
\usage{
convert_FASTA_to_BAPS(data)
}
\arguments{
\item{data}{dataset to be converted}
}
\value{
`data` in BAPS format
}
\description{
Converts an R object from FASTA to BAPS format
}
\examples{
data <- system.file("extdata", "FASTA_clustering_diploid.fasta", package = "rBAPS")
convert_FASTA_to_BAPS(data)
}
\author{
Waldir Leoncio
}