preprocessing_scaffold: replace Missing Value with NA

R/globals.R

@@ -1,21 +1,3 @@
-##
-## msDiaLogue: Analysis + Visuals for Data Indep. Aquisition Mass Spectrometry Data
-## Copyright (C) 2024  Shiying Xiao, Timothy Moore and Charles Watt
-## Shiying Xiao <shiying.xiao@uconn.edu>
-##
-## This file is part of the R package msDiaLogue.
-##
-## The R package msDiaLogue is free software: You can redistribute it and/or
-## modify it under the terms of the GNU General Public License as published by
-## the Free Software Foundation, either version 3 of the License, or any later
-## version (at your option). See the GNU General Public License at
-## <https://www.gnu.org/licenses/> for details.
-##
-## The R package wdnet is distributed in the hope that it will be useful,
-## but WITHOUT ANY WARRANTY without even the implied warranty of
-## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-##
-
 # Generated by roxyglobals: do not edit by hand
 
 utils::globalVariables(c(

R/preprocessing.R

@@ -260,6 +260,7 @@ preprocessing_scaffold <- function(fileName, dataSet = NULL) {
   ## select columns necessary for analysis
   selectedData <- dataSet %>%
     select(-infoColName[infoColName != "ProteinAccessions"]) %>%
+    mutate(across(-ProteinAccessions, ~as.numeric(replace(., . == "Missing Value", NA)))) %>%
     pivot_longer(-ProteinAccessions, names_to = "ConditionReplicate", values_to = "Quantity") %>%
     # gather(ConditionReplicate, Quantity, -ProteinAccessions) %>%
     mutate(ConditionReplicate = sub(".+_(.+)", "\\1", ConditionReplicate)) %>%

docs/pkgdown.yml

@@ -4,7 +4,7 @@ pkgdown_sha: ~
 articles:
   scaffold: scaffold.html
   usage_template: usage_template.html
-last_built: 2024-04-18T05:37Z
+last_built: 2024-04-24T17:42Z
 urls:
   reference: https://uconn-scs.github.io/msDiaLogue/reference
   article: https://uconn-scs.github.io/msDiaLogue/articles