diff --git a/DESCRIPTION b/DESCRIPTION
index 2bdd7b4d16640c69bade9dabada01b5113cb01fd..734d7dc24c8178fe517205fe959ae568cae3347c 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -27,7 +27,8 @@ Imports:
purrr,
tibble,
changepoint,
- GenomicRanges
+ GenomicRanges,
+ plyranges
Suggests:
rmarkdown,
knitr,
diff --git a/NAMESPACE b/NAMESPACE
index d5ab6dfe98f455cdc158622b01809ccd22543915..cddcbd931c945c0b7b8d2fbf4cc79d4183919bbf 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -10,6 +10,7 @@ export(extract_ranges)
export(find_cpts)
export(merge_segments)
export(normalise_lr)
+export(read_axiom)
export(read_confidences)
export(read_summary)
export(regroup_data)
diff --git a/R/read_axiom.R b/R/read_axiom.R
new file mode 100644
index 0000000000000000000000000000000000000000..ba0b22f09672e6d2f0e6b1256c80e7e03e566433
--- /dev/null
+++ b/R/read_axiom.R
@@ -0,0 +1,93 @@
+#' Read Axiom genotyping output files
+#'
+#' @param path path to folder containing the files
+#' @param read_conf whether or not to read the AxiomGT1.confidences.txt file (defaults to FALSE)
+#'
+#' @import dplyr
+#' @import readr
+#' @import stringr
+#'
+#' @return A [tibble()].
+#' @export
+#'
+#' @examples
+#' \dontrun{
+#' read_axiom(path, read_conf = FALSE)
+#' }
+
+read_axiom <- function(path, read_conf = FALSE) {
+
+ # Set NULL variables
+ "." <- NULL
+
+ # Check if all Axiom files exist in the folder
+
+ message("Checking if Axiom files exist in the folder")
+
+ if(!file.exists(paste0(path, "AxiomGT1.calls.final.txt"))) {
+ stop("AxiomGT1.calls.final.txt missing")
+ }
+
+ if(read_conf == TRUE) {
+ if(!file.exists(paste0(path, "AxiomGT1.confidences.txt"))) {
+ stop("AxiomGT1.confidences.txt missing")
+ }
+ }
+
+ if(!file.exists(paste0(path, "AxiomGT1.summary.txt"))) {
+ stop("AxiomGT1.summary.txt missing")
+ }
+
+ # Read AxiomGT1.calls.final.txt -> 'calls'
+
+ message("Reading AxiomGT1.calls.final.txt")
+
+ calls <- readr::read_tsv(paste0(path, "AxiomGT1.calls.final.txt"),
+ show_col_types = FALSE)
+ assign(x = "calls", value = calls, pos = ".GlobalEnv")
+
+ # Read AxiomGT1.confidences.txt -> 'confidences'
+
+ if(read_conf == TRUE) {
+
+ message("Reading AxiomGT1.confidences.txt")
+
+ conf_colnames <- readr::read_lines(file = paste0(path, "AxiomGT1.confidences.txt"),
+ skip = (grep(pattern = "^probeset_id",
+ x = readLines(paste0(path, "AxiomGT1.confidences.txt"))) - 1),
+ n_max = 1) |>
+ stringr::str_split(pattern = "\t") |>
+ unlist()
+
+ confidences <- vroom::vroom(file = paste0(path, "AxiomGT1.confidences.txt"),
+ delim = "\t",
+ comment = "#",
+ col_names = conf_colnames,
+ show_col_types = FALSE) |>
+ dplyr::filter(probeset_id != "probeset_id")
+
+ assign(x = "confidences", value = confidences, pos = ".GlobalEnv")
+
+ }
+
+ # Read AxiomGT1.summary.txt -> 'summary'
+
+ message("Reading AxiomGT1.summary.txt")
+
+ summary_colnames <- readr::read_lines(file = paste0(path, "AxiomGT1.summary.txt"),
+ skip = (grep(pattern = "^probeset_id",
+ x = readLines(paste0(path, "AxiomGT1.summary.txt"))) - 1),
+ n_max = 1) |>
+ stringr::str_split(pattern = "\t") |>
+ unlist()
+
+ summary <- vroom::vroom(file = paste0(path, "AxiomGT1.summary.txt"),
+ delim = "\t",
+ comment = "#",
+ col_names = summary_colnames,
+ show_col_types = FALSE) |>
+ dplyr::filter(probeset_id != "probeset_id")
+
+ assign(x = "summary", value = summary, pos = ".GlobalEnv")
+
+}
diff --git a/R/read_confidences.R b/R/read_confidences.R
deleted file mode 100644
index 561fdefedc43c4ccc268b77232711c99c55356b8..0000000000000000000000000000000000000000
--- a/R/read_confidences.R
+++ /dev/null
@@ -1,38 +0,0 @@
-#' Read confidences file from genotyping pipeline output
-#'
-#' @param confidences_file path to confidences file
-#'
-#' @import dplyr
-#' @import readr
-#' @import stringr
-#'
-#' @return A [tibble()].
-#' @export
-#'
-#' @examples
-#' \dontrun{
-#' read_confidences(confidences_file)
-#' }
-
-read_confidences <- function(confidences_file) {
-
- # Set NULL variables
- probeset_id <- "." <- NULL
-
- # Extract column names
- colnames <- readr::read_lines(confidences_file) %>%
- subset(grepl(pattern = "^probeset_id*", .)) %>%
- stringr::str_split(pattern = "\t") %>%
- unlist()
-
- # Read file
- confidences_data <- readr::read_delim(file = confidences_file,
- delim = "\t",
- comment = "#",
- col_names = colnames) %>%
- filter(probeset_id != "probeset_id")
-
- # Set column names
- #names(summary_data) <- col_names
-
-}
diff --git a/R/read_summary.R b/R/read_summary.R
deleted file mode 100644
index 1ad2ac337a84dc3a88ff6f1f35cd7806b58c41de..0000000000000000000000000000000000000000
--- a/R/read_summary.R
+++ /dev/null
@@ -1,37 +0,0 @@
-#' Read summary file from genotyping pipeline output
-#'
-#' @param summary_file path to summary file
-#'
-#' @import dplyr
-#' @import readr
-#' @import stringr
-#'
-#' @return A [tibble()].
-#' @export
-#'
-#' @examples
-#' \dontrun{
-#' read_summary(summary_file)
-#' }
-
-read_summary <- function(summary_file) {
-
- # Set NULL variables
- "." <- NULL
-
- # Extract column names
- colnames <- readr::read_lines(summary_file) %>%
- subset(grepl(pattern = "^probeset_id*", .)) %>%
- stringr::str_split(pattern = "\t") %>%
- unlist()
-
- # Read file
- summary_data <- readr::read_delim(file = summary_file,
- delim = "\t",
- comment = "#",
- col_names = colnames)
-
- # Set column names
- #names(summary_data) <- col_names
-
-}
diff --git a/man/read_axiom.Rd b/man/read_axiom.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..791003de374a56acad9bf5a94584b28dbdf0e15a
--- /dev/null
+++ b/man/read_axiom.Rd
@@ -0,0 +1,24 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/read_axiom.R
+\name{read_axiom}
+\alias{read_axiom}
+\title{Read Axiom genotyping output files}
+\usage{
+read_axiom(path, read_conf = FALSE)
+}
+\arguments{
+\item{path}{path to folder containing the files}
+
+\item{read_conf}{whether or not to read the AxiomGT1.confidences.txt file (defaults to FALSE)}
+}
+\value{
+A \code{\link[=tibble]{tibble()}}.
+}
+\description{
+Read Axiom genotyping output files
+}
+\examples{
+\dontrun{
+read_axiom(path, read_conf = FALSE)
+}
+}