From 7b8e6df5746750b987304b4f6be5db25eda62ae9 Mon Sep 17 00:00:00 2001
From: Jonathan Kitt <jonathan.kitt@inrae.fr>
Date: Thu, 30 Jan 2025 16:57:53 +0100
Subject: [PATCH 1/2] fix bug in detect_cpts()
---
R/detect_cpts.R | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/R/detect_cpts.R b/R/detect_cpts.R
index 1beea41..12c86ad 100644
--- a/R/detect_cpts.R
+++ b/R/detect_cpts.R
@@ -32,7 +32,7 @@ detect_cpts <- function(lr, file_name = NULL, chromosome = NULL,
# Set NULL variables
- chromosome <- file_name <- position <- NULL
+ chromosome <- file_name <- position <- lr_sub <- NULL
# Extract list of samples
--
GitLab
From 7f7f6228444aafcbf3c6810b9332d28b16004eb2 Mon Sep 17 00:00:00 2001
From: Jonathan Kitt <jonathan.kitt@inrae.fr>
Date: Mon, 3 Feb 2025 11:18:17 +0100
Subject: [PATCH 2/2] update read_axiom() function: read Axiom files, add SNPs,
remove unmapped SNPs & arrange data
---
R/read_axiom.R | 109 ++++++++++++++++++++++++++++++++++++++++++----
man/read_axiom.Rd | 6 ++-
2 files changed, 106 insertions(+), 9 deletions(-)
diff --git a/R/read_axiom.R b/R/read_axiom.R
index ba0b22f..cbf45fd 100644
--- a/R/read_axiom.R
+++ b/R/read_axiom.R
@@ -2,8 +2,11 @@
#'
#' @param path path to folder containing the files
#' @param read_conf whether or not to read the AxiomGT1.confidences.txt file (defaults to FALSE)
+#' @param snp_file file containing the list of SNPs (must have 3 columns, 'probeset_id', 'chromosome', 'position')
+#' @param rm_unmapped whether or not to remove unmapped SNPs (defaults to FALSE)
#'
#' @import dplyr
+#' @import tidyr
#' @import readr
#' @import stringr
#'
@@ -15,10 +18,10 @@
#' read_axiom(path, read_conf = FALSE)
#' }
-read_axiom <- function(path, read_conf = FALSE) {
+read_axiom <- function(path, read_conf = FALSE, snp_file = NULL, rm_unmapped = FALSE) {
# Set NULL variables
- "." <- NULL
+ # "." <- NULL
# Check if all Axiom files exist in the folder
@@ -43,8 +46,10 @@ read_axiom <- function(path, read_conf = FALSE) {
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")
+ show_col_types = FALSE) |>
+ tidyr::pivot_longer(cols = -probeset_id,
+ names_to = "file_name",
+ values_to = "genotyping_call")
# Read AxiomGT1.confidences.txt -> 'confidences'
@@ -64,9 +69,10 @@ read_axiom <- function(path, read_conf = FALSE) {
comment = "#",
col_names = conf_colnames,
show_col_types = FALSE) |>
- dplyr::filter(probeset_id != "probeset_id")
-
- assign(x = "confidences", value = confidences, pos = ".GlobalEnv")
+ dplyr::filter(probeset_id != "probeset_id") |>
+ tidyr::pivot_longer(cols = -probeset_id,
+ names_to = "file_name",
+ values_to = "confidence_score")
}
@@ -88,6 +94,93 @@ read_axiom <- function(path, read_conf = FALSE) {
show_col_types = FALSE) |>
dplyr::filter(probeset_id != "probeset_id")
- assign(x = "summary", value = summary, pos = ".GlobalEnv")
+ # Extract A signal from summary file
+
+ signal_a <- summary |>
+ dplyr::filter(!grepl(pattern = "NP", x = probeset_id)) |>
+ dplyr::filter(grepl("AX-[0-9]*-A", probeset_id)) |>
+ dplyr::mutate(probeset_id = stringr::str_remove(string = probeset_id, pattern = "-A")) |>
+ tidyr::pivot_longer(cols = -probeset_id,
+ names_to = "file_name",
+ values_to = "signal_a")
+
+ # Extract B signal from summary file
+
+ signal_b <- summary |>
+ dplyr::filter(!grepl(pattern = "NP", x = probeset_id)) |>
+ dplyr::filter(grepl("AX-[0-9]*-B", probeset_id)) |>
+ dplyr::mutate(probeset_id = stringr::str_remove(string = probeset_id, pattern = "-B")) |>
+ tidyr::pivot_longer(cols = -probeset_id,
+ names_to = "file_name",
+ values_to = "signal_b")
+
+ # Regroup all Axiom data
+
+ message("Regrouping Axiom data")
+
+ axiom_data <- signal_a |>
+ dplyr::left_join(signal_b, by = c("probeset_id", "file_name")) |>
+ dplyr::left_join(calls, by = c("probeset_id", "file_name"))
+
+ if (read_conf == TRUE & !is.null(snp_file)) {
+
+ message("Adding SNPs")
+
+ snps <- readr::read_delim(snp_file, show_col_types = FALSE) |>
+ dplyr::select(probeset_id, chromosome, position)
+
+ axiom_data <- axiom_data |>
+ dplyr::left_join(confidences, by = c("probeset_id", "file_name")) |>
+ dplyr::left_join(snps, by = "probeset_id") |>
+ dplyr::select(file_name, probeset_id, chromosome, position, confidence_score,
+ signal_a, signal_b, genotyping_call) |>
+ dplyr::arrange(file_name, chromosome, position)
+
+ }
+
+ if (read_conf == TRUE & is.null(snp_file)) {
+
+ axiom_data <- axiom_data |>
+ dplyr::left_join(confidences, by = c("probeset_id", "file_name")) |>
+ dplyr::select(file_name, probeset_id, confidence_score,
+ signal_a, signal_b, genotyping_call) |>
+ dplyr::arrange(file_name, probeset_id)
+
+ }
+
+ if (read_conf == FALSE & !is.null(snp_file)) {
+
+ message("Adding SNPs")
+
+ snps <- readr::read_delim(snp_file, show_col_types = FALSE) |>
+ dplyr::select(probeset_id, chromosome, position)
+
+ axiom_data <- axiom_data |>
+ dplyr::left_join(snps, by = "probeset_id") |>
+ dplyr::select(file_name, probeset_id, chromosome, position,
+ signal_a, signal_b, genotyping_call) |>
+ dplyr::arrange(file_name, chromosome, position)
+
+ }
+
+ if (read_conf == FALSE & is.null(snp_file)) {
+
+ axiom_data <- axiom_data |>
+ dplyr::select(file_name, probeset_id,
+ signal_a, signal_b, genotyping_call) |>
+ dplyr::arrange(file_name, probeset_id)
+
+ }
+
+ if (!is.null(snp_file) & rm_unmapped == TRUE) {
+
+ message("Removing unmapped SNPs")
+
+ axiom_data <- axiom_data |>
+ tidyr::drop_na(chromosome, position)
+
+ }
+
+ return(axiom_data)
}
diff --git a/man/read_axiom.Rd b/man/read_axiom.Rd
index 791003d..2e56f71 100644
--- a/man/read_axiom.Rd
+++ b/man/read_axiom.Rd
@@ -4,12 +4,16 @@
\alias{read_axiom}
\title{Read Axiom genotyping output files}
\usage{
-read_axiom(path, read_conf = FALSE)
+read_axiom(path, read_conf = FALSE, snp_file = NULL, rm_unmapped = 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)}
+
+\item{snp_file}{file containing the list of SNPs (must have 3 columns, 'probeset_id', 'chromosome', 'position')}
+
+\item{rm_unmapped}{whether or not to remove unmapped SNPs (defaults to FALSE)}
}
\value{
A \code{\link[=tibble]{tibble()}}.
--
GitLab