diff --git a/NAMESPACE b/NAMESPACE index cddcbd931c945c0b7b8d2fbf4cc79d4183919bbf..23a2879f70b2c867c124ba1507cdb8e566287606 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -4,15 +4,11 @@ export(calculate_lr) export(calculate_maf) export(count_alleles) export(count_confidences) -export(extract_a) -export(extract_b) export(extract_ranges) export(find_cpts) export(merge_segments) export(normalise_lr) export(read_axiom) -export(read_confidences) -export(read_summary) export(regroup_data) export(summarise_segments) export(transform_lr) diff --git a/R/calculate_lr.R b/R/calculate_lr.R index 32291bd0553b7227ccc78bb42f5b492be85b8aac..076e8ef1e45b00bac26e8a7129ad22c23b3aadb9 100644 --- a/R/calculate_lr.R +++ b/R/calculate_lr.R @@ -1,7 +1,7 @@ -#' Calculate lr values from signal A and signal B +#' Calculate lr values from summary file #' -#' @param signal_a signal_a values -#' @param signal_b signal_b values +#' @param summary_file imported summary file (usually named 'summary') +#' @param format "wide" or "long" table (defaults to "long") #' #' @import dplyr #' @import tidyr @@ -11,25 +11,52 @@ #' #' @examples #' \dontrun{ -#' calculate_lr(signal_a, signal_b) +#' calculate_lr(summary_file, format = "long") #' } -calculate_lr <- function(signal_a, signal_b) { +calculate_lr <- function(summary_file, format = "long") { # Set NULL variables a <- b <- pivot_longer <- probeset_id <- NULL - # Transform to long format + # Extract A signal from summary file + message("Extracting A signal from summary file") + signal_a <- summary_file |> + 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") - signal_a_lg <- signal_a %>% - tidyr::pivot_longer(!probeset_id, names_to = "file_name", values_to = "a") - - signal_b_lg <- signal_b %>% - tidyr::pivot_longer(!probeset_id, names_to = "file_name", values_to = "b") + # Extract B signal from summary file + message("Extracting B signal from summary file") + signal_b <- summary_file |> + 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") # Calculate lr values - dplyr::left_join(signal_a_lg, signal_b_lg) %>% - dplyr::mutate(lr = log2(sqrt(a^2 + b^2))) %>% - dplyr::select(-c(a, b)) + message("Calculating lr values") + lr <- signal_a |> + dplyr::left_join(signal_b) |> + dplyr::mutate(lr = log2(sqrt(signal_a^2 + signal_b^2)), + .keep = "unused") + + # If format is set to "wide", transform the table + if (format == "wide") { + message("Pivoting output table to wide format") + lr <- lr |> + tidyr::pivot_wider(id_cols = probeset_id, + names_from = file_name, + values_from = lr) + } + + # Assign to Global Environment + assign(x = "lr", value = lr, pos = ".GlobalEnv") + } diff --git a/R/extract_a.R b/R/extract_a.R deleted file mode 100644 index c59a4f81ec81f8e2cbff6071ad380878bd3e5288..0000000000000000000000000000000000000000 --- a/R/extract_a.R +++ /dev/null @@ -1,27 +0,0 @@ -#' Extract signal A values from summary file -#' -#' @param summary_file summary file -#' -#' @import dplyr -#' -#' @return A [tibble()]. -#' @export -#' -#' @examples -#' \dontrun{ -#' extract_a(summary_file) -#' } - -extract_a <- function(summary_file) { - - # Set NULL variables - - probeset_id <- NULL - - # Extract signal A values - - signal_a <- summary_file %>% - subset(!grepl(pattern = "NP", probeset_id)) %>% - subset(grepl("AX-[0-9]*-A", probeset_id)) %>% - dplyr::mutate(probeset_id = gsub(pattern = "-A", replacement = "", x = probeset_id)) -} diff --git a/R/extract_b.R b/R/extract_b.R deleted file mode 100644 index c4f5b9e9de17c2e81e637af7ac019a6a5cfb21ee..0000000000000000000000000000000000000000 --- a/R/extract_b.R +++ /dev/null @@ -1,27 +0,0 @@ -#' Extract signal B values from summary file -#' -#' @param summary_file summary file -#' -#' @import dplyr -#' -#' @return A [tibble()]. -#' @export -#' -#' @examples -#' \dontrun{ -#' extract_b(summary_file) -#' } - -extract_b <- function(summary_file) { - - # Set NULL variables - - probeset_id <- NULL - - # Extract signal B values - - signal_b <- summary_file %>% - subset(!grepl(pattern = "NP", probeset_id)) %>% - subset(grepl("AX-[0-9]*-B", probeset_id)) %>% - dplyr::mutate(probeset_id = gsub(pattern = "-B", replacement = "", x = probeset_id)) -} diff --git a/man/calculate_lr.Rd b/man/calculate_lr.Rd index 7c21481d549322f83502ea5f082add04ff8cd537..38748af93ba130eb9f5b08d9252228f9413da475 100644 --- a/man/calculate_lr.Rd +++ b/man/calculate_lr.Rd @@ -2,23 +2,23 @@ % Please edit documentation in R/calculate_lr.R \name{calculate_lr} \alias{calculate_lr} -\title{Calculate lr values from signal A and signal B} +\title{Calculate lr values from summary file} \usage{ -calculate_lr(signal_a, signal_b) +calculate_lr(summary_file, format = "long") } \arguments{ -\item{signal_a}{signal_a values} +\item{summary_file}{imported summary file (usually named 'summary')} -\item{signal_b}{signal_b values} +\item{format}{"wide" or "long" table (defaults to "long")} } \value{ A \code{\link[=tibble]{tibble()}}. } \description{ -Calculate lr values from signal A and signal B +Calculate lr values from summary file } \examples{ \dontrun{ -calculate_lr(signal_a, signal_b) +calculate_lr(summary_file, format = "long") } } diff --git a/man/extract_a.Rd b/man/extract_a.Rd deleted file mode 100644 index 274455e960c21de2db4e38358885def838c7addb..0000000000000000000000000000000000000000 --- a/man/extract_a.Rd +++ /dev/null @@ -1,22 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/extract_a.R -\name{extract_a} -\alias{extract_a} -\title{Extract signal A values from summary file} -\usage{ -extract_a(summary_file) -} -\arguments{ -\item{summary_file}{summary file} -} -\value{ -A \code{\link[=tibble]{tibble()}}. -} -\description{ -Extract signal A values from summary file -} -\examples{ -\dontrun{ -extract_a(summary_file) -} -} diff --git a/man/extract_b.Rd b/man/extract_b.Rd deleted file mode 100644 index f9e8410aae7f5f8c68dd214e4872eea1e2355824..0000000000000000000000000000000000000000 --- a/man/extract_b.Rd +++ /dev/null @@ -1,22 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/extract_b.R -\name{extract_b} -\alias{extract_b} -\title{Extract signal B values from summary file} -\usage{ -extract_b(summary_file) -} -\arguments{ -\item{summary_file}{summary file} -} -\value{ -A \code{\link[=tibble]{tibble()}}. -} -\description{ -Extract signal B values from summary file -} -\examples{ -\dontrun{ -extract_b(summary_file) -} -} diff --git a/man/read_confidences.Rd b/man/read_confidences.Rd deleted file mode 100644 index a5f9b905c46eb68e4875984db07bc44450f195bb..0000000000000000000000000000000000000000 --- a/man/read_confidences.Rd +++ /dev/null @@ -1,22 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/read_confidences.R -\name{read_confidences} -\alias{read_confidences} -\title{Read confidences file from genotyping pipeline output} -\usage{ -read_confidences(confidences_file) -} -\arguments{ -\item{confidences_file}{path to confidences file} -} -\value{ -A \code{\link[=tibble]{tibble()}}. -} -\description{ -Read confidences file from genotyping pipeline output -} -\examples{ -\dontrun{ -read_confidences(confidences_file) -} -} diff --git a/man/read_summary.Rd b/man/read_summary.Rd deleted file mode 100644 index 2ec67088f59c948bb153752c259900af4f388e4f..0000000000000000000000000000000000000000 --- a/man/read_summary.Rd +++ /dev/null @@ -1,22 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/read_summary.R -\name{read_summary} -\alias{read_summary} -\title{Read summary file from genotyping pipeline output} -\usage{ -read_summary(summary_file) -} -\arguments{ -\item{summary_file}{path to summary file} -} -\value{ -A \code{\link[=tibble]{tibble()}}. -} -\description{ -Read summary file from genotyping pipeline output -} -\examples{ -\dontrun{ -read_summary(summary_file) -} -}