diff --git a/NAMESPACE b/NAMESPACE
index db39276a..b25f6c6f 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -26,7 +26,6 @@ export(MissingHelpers)
export(Model)
export(ModelInterface)
export(ProjectStructure)
-export(ProteinAnnotation)
export(R6_extract_values)
export(UpSet_interaction_missing_stats)
export(UpSet_missing_stats)
diff --git a/R/ProteinAnnotation.R b/R/ProteinAnnotation.R
deleted file mode 100644
index 417a5434..00000000
--- a/R/ProteinAnnotation.R
+++ /dev/null
@@ -1,125 +0,0 @@
-# ProteinAnnotation ----
-#' Decorates LFQData with a row annotation and some protein specific functions.
-#'
-#' @export
-#' @family LFQData
-#' @examples
-#'
-#' istar <-prolfqua::sim_lfq_data_peptide_config()
-#' lfqdata <- LFQData$new(istar$data, istar$config)
-#' pannot <- ProteinAnnotation$new( lfqdata )
-#' pannot$annotate_decoys()
-#' pannot$annotate_contaminants()
-#' dd <- pannot$clean()
-#' tmp <- lfqdata$get_subset(dd)
-#' pannot$row_annot
-#'
-ProteinAnnotation <-
- R6::R6Class("ProteinAnnotation",
- public = list(
- #' @field row_annot data.frame containing further information
- row_annot = NULL,
- #' @field pID column with protein ids
- pID = character(),
- #' @field description name of column containing descriptions
- description = "description",
- #' @field cleaned_ids vector with columns containing addition IDs
- cleaned_ids = character(),
- #' @field nr_children name of columns with the number of peptides
- nr_children = character(),
- #' @description initialize
- #' @param lfqdata data frame from \code{\link{setup_analysis}}
- #' @param row_annot data frame with row annotation. Must have columns matching \code{config$table$hierarchy_keys_depth()}
- #' @param description name of column with description
- #' @param ids names of columns with cleaned Ids
- #' @param nr_peptides additional peptides
- #' @param nr_children column with the number of children
- initialize = function(lfqdata,
- row_annot = NULL,
- description = NULL,
- ids = NULL,
- nr_children = "nr_peptides"){
- self$pID = lfqdata$config$table$hierarchy_keys_depth()[1]
- self$nr_children = nr_children
- if ( !is.null(ids)) {self$cleaned_ids = ids} else {self$cleaned_ids = self$pID}
- if ( !is.null(description)) {self$description = description} else {self$description = self$pID}
- if ( !is.null(row_annot)) {
- stopifnot(self$pID %in% colnames(row_annot))
- row_annot <- dplyr::filter(row_annot, !!sym(self$pID) %in% lfqdata$data[[self$pID]] )
- self$row_annot <- row_annot
- } else {
- self$row_annot <- distinct(select(lfqdata$data, self$pID))
- }
-
- stopifnot(self$cleaned_ids %in% colnames(self$row_annot))
- stopifnot(self$description %in% colnames(self$row_annot))
-
- if (!self$nr_children %in% colnames(row_annot) ) {
- warning("no nr_children column specified, computing using nr_obs_experiment function")
- self$row_annot <- inner_join(
- self$row_annot,
- nr_obs_experiment(lfqdata$data, lfqdata$config, name_nr_child = self$nr_children),
- by = self$pID)
- }
- },
- #' @description
- #' annotate rev sequences
- #' @param pattern default "REV_"
- annotate_decoys = function(pattern = "REV_") {
- self$row_annot <- self$row_annot |> mutate(
- REV = case_when(grepl(pattern, !!sym(self$pID), ignore.case = TRUE) ~ TRUE,
- TRUE ~ FALSE))
-
- return(sum(self$row_annot$REV))
- },
- #' @description
- #' annotate contaminants
- #' @param pattern default "^zz|^CON"
- annotate_contaminants = function(pattern = "^zz|^CON") {
- self$row_annot <- self$row_annot |> mutate(
- CON = case_when(grepl(pattern, !!sym(self$pID), ignore.case = TRUE) ~ TRUE,
- TRUE ~ FALSE))
- return(sum(self$row_annot$CON))
- },
- #' @description get number of neither contaminants nor decoys
- #' @param contaminants remove contaminants
- #' @param decoys remove decoys
- #' return number of cleans
- nr_clean = function(contaminants = TRUE, decoys = TRUE){
-
- if (decoys && !("REV" %in% colnames(self$row_annot)) ) { stop("annotate REV") }
- if (contaminants & !("CON" %in% colnames(self$row_annot)) ) { stop("annotate CON") }
-
- res <- if (decoys && contaminants) {
- sum(!self$row_annot$REV & !self$row_annot$CON)
- } else if (contaminants) {
- sum(!self$row_annot$CON)
- } else if (decoys) {
- sum(!self$row_annot$REV)
- } else {
- nrow(self$row_annot)
- }
- return(res)
- },
- #' @description remove REV and CON sequences
- #' @param contaminants remove contaminants
- #' @param decoys remove decoys
- #'
- clean = function(contaminants = TRUE, decoys = TRUE){
- if (contaminants && !("REV" %in% colnames(self$row_annot)) ) { stop("annotate REV") }
- if (decoys && !("CON" %in% colnames(self$row_annot)) ) { stop("annotate CON") }
- res <- if (decoys && contaminants) {
- filter(self$row_annot , !self$row_annot$REV & !self$row_annot$CON )
- } else if (contaminants) {
- filter(self$row_annot , !self$row_annot$CON)
- } else if (decoys) {
- filter(self$row_annot , !self$row_annot$REV )
- } else {
- self$row_annot
- }
- return(res)
- }
-
- )
- )
-
diff --git a/man/LFQData.Rd b/man/LFQData.Rd
index 22aecc32..743e1e09 100644
--- a/man/LFQData.Rd
+++ b/man/LFQData.Rd
@@ -64,8 +64,7 @@ Other LFQData:
\code{\link{LFQDataStats}},
\code{\link{LFQDataSummariser}},
\code{\link{LFQDataToSummarizedExperiment}()},
-\code{\link{LFQDataWriter}},
-\code{\link{ProteinAnnotation}}
+\code{\link{LFQDataWriter}}
}
\concept{LFQData}
\section{Public fields}{
diff --git a/man/LFQDataAggregator.Rd b/man/LFQDataAggregator.Rd
index ffd6c6fd..c21dbd31 100644
--- a/man/LFQDataAggregator.Rd
+++ b/man/LFQDataAggregator.Rd
@@ -53,8 +53,7 @@ Other LFQData:
\code{\link{LFQDataStats}},
\code{\link{LFQDataSummariser}},
\code{\link{LFQDataToSummarizedExperiment}()},
-\code{\link{LFQDataWriter}},
-\code{\link{ProteinAnnotation}}
+\code{\link{LFQDataWriter}}
}
\concept{LFQData}
\section{Public fields}{
diff --git a/man/LFQDataPlotter.Rd b/man/LFQDataPlotter.Rd
index b4a5a98a..00fe9bdf 100644
--- a/man/LFQDataPlotter.Rd
+++ b/man/LFQDataPlotter.Rd
@@ -54,8 +54,7 @@ Other LFQData:
\code{\link{LFQDataStats}},
\code{\link{LFQDataSummariser}},
\code{\link{LFQDataToSummarizedExperiment}()},
-\code{\link{LFQDataWriter}},
-\code{\link{ProteinAnnotation}}
+\code{\link{LFQDataWriter}}
}
\concept{LFQData}
\keyword{static}
diff --git a/man/LFQDataStats.Rd b/man/LFQDataStats.Rd
index 7e2ca682..5ee310c3 100644
--- a/man/LFQDataStats.Rd
+++ b/man/LFQDataStats.Rd
@@ -71,8 +71,7 @@ Other LFQData:
\code{\link{LFQDataPlotter}},
\code{\link{LFQDataSummariser}},
\code{\link{LFQDataToSummarizedExperiment}()},
-\code{\link{LFQDataWriter}},
-\code{\link{ProteinAnnotation}}
+\code{\link{LFQDataWriter}}
}
\concept{LFQData}
\section{Public fields}{
diff --git a/man/LFQDataSummariser.Rd b/man/LFQDataSummariser.Rd
index 532853d1..8b596fef 100644
--- a/man/LFQDataSummariser.Rd
+++ b/man/LFQDataSummariser.Rd
@@ -36,8 +36,7 @@ Other LFQData:
\code{\link{LFQDataPlotter}},
\code{\link{LFQDataStats}},
\code{\link{LFQDataToSummarizedExperiment}()},
-\code{\link{LFQDataWriter}},
-\code{\link{ProteinAnnotation}}
+\code{\link{LFQDataWriter}}
}
\concept{LFQData}
\section{Public fields}{
diff --git a/man/LFQDataToSummarizedExperiment.Rd b/man/LFQDataToSummarizedExperiment.Rd
index 28afe940..0bbd217f 100644
--- a/man/LFQDataToSummarizedExperiment.Rd
+++ b/man/LFQDataToSummarizedExperiment.Rd
@@ -34,7 +34,6 @@ Other LFQData:
\code{\link{LFQDataPlotter}},
\code{\link{LFQDataStats}},
\code{\link{LFQDataSummariser}},
-\code{\link{LFQDataWriter}},
-\code{\link{ProteinAnnotation}}
+\code{\link{LFQDataWriter}}
}
\concept{LFQData}
diff --git a/man/LFQDataWriter.Rd b/man/LFQDataWriter.Rd
index 7744cc1c..8973614f 100644
--- a/man/LFQDataWriter.Rd
+++ b/man/LFQDataWriter.Rd
@@ -17,8 +17,7 @@ Other LFQData:
\code{\link{LFQDataPlotter}},
\code{\link{LFQDataStats}},
\code{\link{LFQDataSummariser}},
-\code{\link{LFQDataToSummarizedExperiment}()},
-\code{\link{ProteinAnnotation}}
+\code{\link{LFQDataToSummarizedExperiment}()}
}
\concept{LFQData}
\section{Public fields}{
diff --git a/man/ProteinAnnotation.Rd b/man/ProteinAnnotation.Rd
deleted file mode 100644
index 5cf59264..00000000
--- a/man/ProteinAnnotation.Rd
+++ /dev/null
@@ -1,183 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/ProteinAnnotation.R
-\name{ProteinAnnotation}
-\alias{ProteinAnnotation}
-\title{Decorates LFQData with a row annotation and some protein specific functions.}
-\description{
-Decorates LFQData with a row annotation and some protein specific functions.
-
-Decorates LFQData with a row annotation and some protein specific functions.
-}
-\examples{
-
-istar <-prolfqua::sim_lfq_data_peptide_config()
-lfqdata <- LFQData$new(istar$data, istar$config)
-pannot <- ProteinAnnotation$new( lfqdata )
-pannot$annotate_decoys()
-pannot$annotate_contaminants()
-dd <- pannot$clean()
-tmp <- lfqdata$get_subset(dd)
-pannot$row_annot
-
-}
-\seealso{
-Other LFQData:
-\code{\link{LFQData}},
-\code{\link{LFQDataAggregator}},
-\code{\link{LFQDataPlotter}},
-\code{\link{LFQDataStats}},
-\code{\link{LFQDataSummariser}},
-\code{\link{LFQDataToSummarizedExperiment}()},
-\code{\link{LFQDataWriter}}
-}
-\concept{LFQData}
-\section{Public fields}{
-\if{html}{\out{}}
-\describe{
-\item{\code{row_annot}}{data.frame containing further information}
-
-\item{\code{pID}}{column with protein ids}
-
-\item{\code{description}}{name of column containing descriptions}
-
-\item{\code{cleaned_ids}}{vector with columns containing addition IDs}
-
-\item{\code{nr_children}}{name of columns with the number of peptides}
-}
-\if{html}{\out{
}}
-}
-\section{Methods}{
-\subsection{Public methods}{
-\itemize{
-\item \href{#method-ProteinAnnotation-new}{\code{ProteinAnnotation$new()}}
-\item \href{#method-ProteinAnnotation-annotate_decoys}{\code{ProteinAnnotation$annotate_decoys()}}
-\item \href{#method-ProteinAnnotation-annotate_contaminants}{\code{ProteinAnnotation$annotate_contaminants()}}
-\item \href{#method-ProteinAnnotation-nr_clean}{\code{ProteinAnnotation$nr_clean()}}
-\item \href{#method-ProteinAnnotation-clean}{\code{ProteinAnnotation$clean()}}
-\item \href{#method-ProteinAnnotation-clone}{\code{ProteinAnnotation$clone()}}
-}
-}
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-ProteinAnnotation-new}{}}}
-\subsection{Method \code{new()}}{
-initialize
-\subsection{Usage}{
-\if{html}{\out{}}\preformatted{ProteinAnnotation$new(
- lfqdata,
- row_annot = NULL,
- description = NULL,
- ids = NULL,
- nr_children = "nr_peptides"
-)}\if{html}{\out{
}}
-}
-
-\subsection{Arguments}{
-\if{html}{\out{}}
-\describe{
-\item{\code{lfqdata}}{data frame from \code{\link{setup_analysis}}}
-
-\item{\code{row_annot}}{data frame with row annotation. Must have columns matching \code{config$table$hierarchy_keys_depth()}}
-
-\item{\code{description}}{name of column with description}
-
-\item{\code{ids}}{names of columns with cleaned Ids}
-
-\item{\code{nr_children}}{column with the number of children}
-
-\item{\code{nr_peptides}}{additional peptides}
-}
-\if{html}{\out{
}}
-}
-}
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-ProteinAnnotation-annotate_decoys}{}}}
-\subsection{Method \code{annotate_decoys()}}{
-annotate rev sequences
-\subsection{Usage}{
-\if{html}{\out{}}\preformatted{ProteinAnnotation$annotate_decoys(pattern = "REV_")}\if{html}{\out{
}}
-}
-
-\subsection{Arguments}{
-\if{html}{\out{}}
-\describe{
-\item{\code{pattern}}{default "REV_"}
-}
-\if{html}{\out{
}}
-}
-}
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-ProteinAnnotation-annotate_contaminants}{}}}
-\subsection{Method \code{annotate_contaminants()}}{
-annotate contaminants
-\subsection{Usage}{
-\if{html}{\out{}}\preformatted{ProteinAnnotation$annotate_contaminants(pattern = "^zz|^CON")}\if{html}{\out{
}}
-}
-
-\subsection{Arguments}{
-\if{html}{\out{}}
-\describe{
-\item{\code{pattern}}{default "^zz|^CON"}
-}
-\if{html}{\out{
}}
-}
-}
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-ProteinAnnotation-nr_clean}{}}}
-\subsection{Method \code{nr_clean()}}{
-get number of neither contaminants nor decoys
-\subsection{Usage}{
-\if{html}{\out{}}\preformatted{ProteinAnnotation$nr_clean(contaminants = TRUE, decoys = TRUE)}\if{html}{\out{
}}
-}
-
-\subsection{Arguments}{
-\if{html}{\out{}}
-\describe{
-\item{\code{contaminants}}{remove contaminants}
-
-\item{\code{decoys}}{remove decoys
-return number of cleans}
-}
-\if{html}{\out{
}}
-}
-}
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-ProteinAnnotation-clean}{}}}
-\subsection{Method \code{clean()}}{
-remove REV and CON sequences
-\subsection{Usage}{
-\if{html}{\out{}}\preformatted{ProteinAnnotation$clean(contaminants = TRUE, decoys = TRUE)}\if{html}{\out{
}}
-}
-
-\subsection{Arguments}{
-\if{html}{\out{}}
-\describe{
-\item{\code{contaminants}}{remove contaminants}
-
-\item{\code{decoys}}{remove decoys}
-}
-\if{html}{\out{
}}
-}
-}
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-ProteinAnnotation-clone}{}}}
-\subsection{Method \code{clone()}}{
-The objects of this class are cloneable with this method.
-\subsection{Usage}{
-\if{html}{\out{}}\preformatted{ProteinAnnotation$clone(deep = FALSE)}\if{html}{\out{
}}
-}
-
-\subsection{Arguments}{
-\if{html}{\out{}}
-\describe{
-\item{\code{deep}}{Whether to make a deep clone.}
-}
-\if{html}{\out{
}}
-}
-}
-}