Fixing memory problems for dataProcess using multicore

DESCRIPTION

@@ -53,7 +53,7 @@ biocViews: ImmunoOncology, MassSpectrometry, Proteomics, Software, Normalization
 LazyData: true
 URL: http://msstats.org
 BugReports: https://groups.google.com/forum/#!forum/msstats
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3
 Encoding: UTF-8
 NeedsCompilation: no
 Packaged: 2017-10-20 02:13:12 UTC; meenachoi

R/RcppExports.R

@@ -2,18 +2,17 @@
 # Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
 
 get_estimable_fixed_random <- function(parameters, contrast) {
-    .Call(`_MSstats_get_estimable_fixed_random`, parameters, contrast)
+  .Call(`_MSstats_get_estimable_fixed_random`, parameters, contrast)
 }
 
 make_contrast_run_quant <- function(input, coefs, contrast_matrix, counts, is_labeled, is_reference = FALSE) {
-    .Call(`_MSstats_make_contrast_run_quant`, input, coefs, contrast_matrix, counts, is_labeled, is_reference)
+  .Call(`_MSstats_make_contrast_run_quant`, input, coefs, contrast_matrix, counts, is_labeled, is_reference)
 }
 
 get_linear_summary <- function(input, coefs, counts, is_labeled) {
-    .Call(`_MSstats_get_linear_summary`, input, coefs, counts, is_labeled)
+  .Call(`_MSstats_get_linear_summary`, input, coefs, counts, is_labeled)
 }
 
 median_polish_summary <- function(x, eps = 0.01, maxiter = 10L) {
-    .Call(`_MSstats_median_polish_summary`, x, eps, maxiter)
+  .Call(`_MSstats_median_polish_summary`, x, eps, maxiter)
 }
-

R/SDRFconverter.R

@@ -1,118 +1,123 @@
 #' Convert SDRF experimental design file into an MSstats annotation file
-#' 
+#'
 #' Takes an SDRF file and outputs an MSstats annotation file. Note
-#' the information in the SDRF file must be correctly annotated for MSstats so 
-#' that MSstats can identify the experimental design. In particular the 
-#' biological replicates must be correctly annotated, with group comparison 
-#' experiments having a unique ID for each BioReplicate. For more information 
-#' on this please see the Supplementary of the most recent  
+#' the information in the SDRF file must be correctly annotated for MSstats so
+#' that MSstats can identify the experimental design. In particular the
+#' biological replicates must be correctly annotated, with group comparison
+#' experiments having a unique ID for each BioReplicate. For more information
+#' on this please see the Supplementary of the most recent
 #' \href{https://pubs.acs.org/doi/10.1021/acs.jproteome.2c00834}{MSstats paper}
-#' 
+#'
 #' @param data SDRF annotation file
-#' @param run_name Column name in SDRF file which contains the name of the MS 
+#' @param run_name Column name in SDRF file which contains the name of the MS
 #' run. The information in this column must match exactly with the run names in
 #' the PSM file
-#' @param condition_name Column name in SDRF file which contains information on 
+#' @param condition_name Column name in SDRF file which contains information on
 #' the conditions in the data.
-#' @param biological_replicate Column name in SDRF file which contains the 
-#' identifier for the biological replicte. Note MSstats uses this column to 
-#' determine if the experiment is a repeated measure design. BioReplicte IDs 
+#' @param biological_replicate Column name in SDRF file which contains the
+#' identifier for the biological replicte. Note MSstats uses this column to
+#' determine if the experiment is a repeated measure design. BioReplicte IDs
 #' should only be reused if the replicate was measured multiple times.
-#' @param fraction Column name in SDFT file which contains information on the 
-#' fractionation in the data. Only required if data contains fractions. Default 
+#' @param fraction Column name in SDFT file which contains information on the
+#' fractionation in the data. Only required if data contains fractions. Default
 #' is `NULL`
-#' 
+#'
 #' @importFrom data.table setDT
-#' 
+#'
 #' @export
-#' 
+#'
 #' @examples
 #' head(example_SDRF)
-#' 
-#' msstats_annotation = SDRFtoAnnotation(example_SDRF)
-#' 
+#'
+#' msstats_annotation <- SDRFtoAnnotation(example_SDRF)
+#'
 #' head(msstats_annotation)
-SDRFtoAnnotation = function(
-        data, 
-        run_name = "comment[data file]",
-        condition_name = "characteristics[disease]",
-        biological_replicate = "characteristics[biological replicate]",
-        fraction = NULL){
-    
-    data = data.table::setDT(data)
-    
-    extract_cols = c(run_name, condition_name, biological_replicate)
-    if (!is.null(fraction)){
-        extract_cols = c(extract_cols, fraction)
-    }
-    colnames(data) = MSstatsConvert:::.standardizeColnames(colnames(data))
-    extract_cols = MSstatsConvert:::.standardizeColnames(extract_cols)
-    
-    data = data[, ..extract_cols]
-    if (length(colnames(data)) < length(extract_cols)){
-        stop("ERROR: One or more of the column passed in the parameters were not found in the data. Please ensure that the column names are correct.")
-    }
-    data.table::setnames(data, extract_cols, 
-                         c("Run", "Condition", "BioReplicate"))
-    
-    return(data)
+SDRFtoAnnotation <- function(data,
+                             run_name = "comment[data file]",
+                             condition_name = "characteristics[disease]",
+                             biological_replicate = "characteristics[biological replicate]",
+                             fraction = NULL) {
+  data <- data.table::setDT(data)
+
+  extract_cols <- c(run_name, condition_name, biological_replicate)
+  if (!is.null(fraction)) {
+    extract_cols <- c(extract_cols, fraction)
+  }
+  colnames(data) <- MSstatsConvert:::.standardizeColnames(colnames(data))
+  extract_cols <- MSstatsConvert:::.standardizeColnames(extract_cols)
+
+  data <- data[, ..extract_cols]
+  if (length(colnames(data)) < length(extract_cols)) {
+    stop("ERROR: One or more of the column passed in the parameters were not found in the data. Please ensure that the column names are correct.")
+  }
+  data.table::setnames(
+    data, extract_cols,
+    c("Run", "Condition", "BioReplicate")
+  )
+
+  return(data)
 }
 
 #' Extract experimental design from MSstats format into SDRF format
-#' 
-#' @param data MSstats formatted data that is the output of a dedicated 
+#'
+#' @param data MSstats formatted data that is the output of a dedicated
 #' converter, such as `MaxQtoMSstatsFormat`, `SkylinetoMSstatsFormat`, ect.
 #' @param run_name Run column name in SDRF data
 #' @param condition_name Condition column name in SDRF data
 #' @param biological_replicate Biological replicate column name in SDRF data
 #' @param fraction Fraction column name in SDRF data (if applicable). Default is
 #' `NULL`. If there are no fractions keep `NULL`.
-#' @param meta_data A data.frame including any additional meta data for the SDRF 
-#' file that is not included in MSstats. This meta data will be added into the 
-#' final SDRF file. Please ensure the run names in the meta data matches the 
+#' @param meta_data A data.frame including any additional meta data for the SDRF
+#' file that is not included in MSstats. This meta data will be added into the
+#' final SDRF file. Please ensure the run names in the meta data matches the
 #' run names in the MSstats data.
-#' 
+#'
 #' @importFrom data.table as.data.table
-#' 
+#'
 #' @export
-#' 
+#'
 #' @examples
-#' mq_ev = data.table::fread(system.file("tinytest/raw_data/MaxQuant/mq_ev.csv",
-#'                                       package = "MSstatsConvert"))
-#' mq_pg = data.table::fread(system.file("tinytest/raw_data/MaxQuant/mq_pg.csv",
-#'                                       package = "MSstatsConvert"))
-#' annot = data.table::fread(system.file("tinytest/raw_data/MaxQuant/annotation.csv",
-#'                                       package = "MSstatsConvert"))
-#' maxq_imported = MaxQtoMSstatsFormat(mq_ev, annot, mq_pg, use_log_file = FALSE)
+#' mq_ev <- data.table::fread(system.file("tinytest/raw_data/MaxQuant/mq_ev.csv",
+#'   package = "MSstatsConvert"
+#' ))
+#' mq_pg <- data.table::fread(system.file("tinytest/raw_data/MaxQuant/mq_pg.csv",
+#'   package = "MSstatsConvert"
+#' ))
+#' annot <- data.table::fread(system.file("tinytest/raw_data/MaxQuant/annotation.csv",
+#'   package = "MSstatsConvert"
+#' ))
+#' maxq_imported <- MaxQtoMSstatsFormat(mq_ev, annot, mq_pg, use_log_file = FALSE)
 #' head(maxq_imported)
-#' 
-#' SDRF_file = extractSDRF(maxq_imported)
-extractSDRF = function(
-        data, 
-        run_name = "comment[data file]",
-        condition_name = "characteristics[disease]",
-        biological_replicate = "characteristics[biological replicate]",
-        fraction = NULL,
-        meta_data = NULL){
-
-    extract_cols = c("Condition", "BioReplicate", "Run", "Fraction")
-    data = as.data.table(data)
-    data = data[, ..extract_cols]
-    data = unique(data)
-
-    if (is.null(fraction)){
-        data$Fraction = NULL
-        data.table::setnames(data, c("Condition", "BioReplicate", "Run"), 
-                 c(run_name, condition_name, biological_replicate))
-    } else {
-        data.table::setnames(data, extract_cols, 
-                 c(run_name, condition_name, biological_replicate, fraction))
-    }
-
-    if (!is.null(meta_data)){
-        meta_data = data.table::setDT(meta_data)
-        data = merge(data, meta_data, all.x = TRUE, all.y = TRUE, by = run_name)
-    }
-
-    return(data)
-}
+#'
+#' SDRF_file <- extractSDRF(maxq_imported)
+extractSDRF <- function(data,
+                        run_name = "comment[data file]",
+                        condition_name = "characteristics[disease]",
+                        biological_replicate = "characteristics[biological replicate]",
+                        fraction = NULL,
+                        meta_data = NULL) {
+  extract_cols <- c("Condition", "BioReplicate", "Run", "Fraction")
+  data <- as.data.table(data)
+  data <- data[, ..extract_cols]
+  data <- unique(data)
+
+  if (is.null(fraction)) {
+    data$Fraction <- NULL
+    data.table::setnames(
+      data, c("Condition", "BioReplicate", "Run"),
+      c(run_name, condition_name, biological_replicate)
+    )
+  } else {
+    data.table::setnames(
+      data, extract_cols,
+      c(run_name, condition_name, biological_replicate, fraction)
+    )
+  }
+
+  if (!is.null(meta_data)) {
+    meta_data <- data.table::setDT(meta_data)
+    data <- merge(data, meta_data, all.x = TRUE, all.y = TRUE, by = run_name)
+  }
+
+  return(data)
+}

R/converters.R

@@ -1,4 +1,4 @@
-# For backwards compatibility, MSstats will export some converters in the 
+# For backwards compatibility, MSstats will export some converters in the
 # MSstats namespace
 
 #' @export
@@ -39,4 +39,4 @@ MSstatsConvert::SkylinetoMSstatsFormat
 
 #' @export
 #' @importFrom MSstatsConvert SpectronauttoMSstatsFormat
-MSstatsConvert::SpectronauttoMSstatsFormat
+MSstatsConvert::SpectronauttoMSstatsFormat