analyze: the texts regarding the reference; minor typo

uconn-scs · Jul 7, 2024 · d342860 · d342860
1 parent 4537788
commit d342860
Show file tree

Hide file tree

Showing 54 changed files with 180 additions and 126 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: msDiaLogue
 Title: Analysis + Visuals for Data Indep. Aquisition Mass Spectrometry Data
-Version: 0.0.4
+Version: 0.0.5
 Authors@R: c(
     person("Shiying", "Xiao", email = "[email protected]",
            role = c("aut", "cre"), comment = c(ORCID = "0000-0002-8846-3258")),

diff --git a/R/analyze.R b/R/analyze.R
@@ -11,7 +11,7 @@
 ## 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,
+## The R package msDiaLogue 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.
 ##
@@ -27,14 +27,27 @@
 #' 
 #' @param dataSet The 2d data set of data.
 #' 
-#' @param conditions A string specifying which two conditions to compare. This argument
-#' only works when there are more than two conditions in \code{dataSet}.
+#' @param conditions A string specifying which two conditions to compare. The order is
+#' important, as the second condition serves as the reference for comparison. When there
+#' are two conditions in \code{dataSet} and this argument is not specified, the
+#' \code{conditions} will automatically be selected by sorting the unique values
+#' alphabetically and in ascending order.
 #' 
 #' @param testType A string (default = "t-test") specifying which statistical test to use:
 #' \enumerate{
-#' \item "t-test": unequal variance t-test.
-#' \item "mod.t-test": moderated t-test \insertCite{smyth2004linear}{msDiaLogue}.
-#' \item "MA": output to plot an MA plot.
+#' \item "t-test": Unequal variance t-test.
+#' \item "mod.t-test": Moderated t-test \insertCite{smyth2004linear}{msDiaLogue}.
+#' \item "MA": Output to plot an MA plot.
+#' }
+#' 
+#' @details
+#' The second condition serves as the reference for comparison. \itemize{
+#' \item "t-test" and "mod.t-test": The differences are calculated by subtracting
+#' the mean of the second condition from the mean of the first condition (Condition 1 -
+#' Condition 2).
+#' \item "MA": The rows are ordered by \code{conditions}. Specifically, the first row
+#' corresponds to the protein-wise average of the first condition, and the second row
+#' corresponds to the second condition.
 #' }
 #' 
 #' @import dplyr
@@ -45,9 +58,7 @@
 #' 
 #' @returns A 2d dataframe includes the following information: \itemize{
 #' \item "t-test" or "mod.t-test": The differences in means and P-values for each protein
-#' between the two conditions. Note that the differences are calculated by subtracting the
-#' mean of the second condition from the mean of the first condition (Condition 1 -
-#' Condition 2).
+#' between the two conditions.
 #' \item "MA": Protein-wise averages within each condition.
 #' }
 #' 
@@ -62,7 +73,7 @@ analyze <- function(dataSet, conditions, testType = "t-test") {
 
   ## check for exactly two conditions
   if (missing(conditions)) {
-    conditions <- unique(dataSet$R.Condition)
+    conditions <- sort(unique(dataSet$R.Condition))
     if (length(conditions) != 2) {
       stop("Please provide exactly two conditions for comparison.")
     }

diff --git a/R/dataMissing.R b/R/dataMissing.R
@@ -11,7 +11,7 @@
 ## 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,
+## The R package msDiaLogue 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.
 ##

diff --git a/R/filterings.R b/R/filterings.R
@@ -11,7 +11,7 @@
 ## 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,
+## The R package msDiaLogue 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.
 ##

diff --git a/R/imputations.R b/R/imputations.R
@@ -11,7 +11,7 @@
 ## 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,
+## The R package msDiaLogue 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.
 ##

diff --git a/R/normalize.R b/R/normalize.R
@@ -6,6 +6,16 @@
 ## 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 msDiaLogue 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.
+##
+
 ###################################
 #### Code for data normalizing ####
 ###################################

diff --git a/R/preprocessing.R b/R/preprocessing.R
@@ -11,7 +11,7 @@
 ## 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,
+## The R package msDiaLogue 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.
 ##

diff --git a/R/pullProteinPath.R b/R/pullProteinPath.R
@@ -11,7 +11,7 @@
 ## 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,
+## The R package msDiaLogue 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.
 ##

diff --git a/R/sortcondition.R b/R/sortcondition.R
@@ -4,6 +4,18 @@
 ## Shiying Xiao <[email protected]>
 ##
 ## 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 msDiaLogue 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.
+##
+
 #' Creating a keyed list of conditions to the list of proteins that are present
 #' 
 #' @description

diff --git a/R/summarize.R b/R/summarize.R
@@ -11,7 +11,7 @@
 ## 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,
+## The R package msDiaLogue 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.
 ##
@@ -34,18 +34,18 @@
 #' @details
 #' The column 'Stat' in the generated data.frame includes the following statistics:
 #' \itemize{
-#' \item n: number.
-#' \item mean: mean.
-#' \item sd: standard deviation.
-#' \item median: median.
-#' \item trimmed: trimmed mean with a trim of 0.1.
-#' \item mad: median absolute deviation (from the median).
-#' \item min: minimum.
-#' \item max: maximum.
-#' \item range: the difference between the maximum and minimum value.
-#' \item skew: skewness.
-#' \item kurtosis: kurtosis.
-#' \item se: standard error.
+#' \item n: Number.
+#' \item mean: Mean.
+#' \item sd: Standard deviation.
+#' \item median: Median.
+#' \item trimmed: Trimmed mean with a trim of 0.1.
+#' \item mad: Median absolute deviation (from the median).
+#' \item min: Minimum.
+#' \item max: Maximum.
+#' \item range: The difference between the maximum and minimum value.
+#' \item skew: Skewness.
+#' \item kurtosis: Kurtosis.
+#' \item se: Standard error.
 #' }
 #' 
 #' @import dplyr

diff --git a/R/transform.R b/R/transform.R
@@ -11,7 +11,7 @@
 ## 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,
+## The R package msDiaLogue 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.
 ##

diff --git a/R/trimFASTA.R b/R/trimFASTA.R
@@ -11,7 +11,7 @@
 ## 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,
+## The R package msDiaLogue 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.
 ##

diff --git a/R/trunc-knn.R b/R/trunc-knn.R
@@ -11,7 +11,7 @@
 ## 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,
+## The R package msDiaLogue 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.
 ##

diff --git a/R/visualizations.R b/R/visualizations.R
@@ -11,7 +11,7 @@
 ## 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,
+## The R package msDiaLogue 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.
 ##
@@ -107,10 +107,10 @@
 #' @param label A text (default = "all") specifying the elements to be labelled when
 #' \code{graphType = "PCA_biplot"}. Allowed values:
 #' \itemize{
-#' \item "all": label both active individuals and active variables.
-#' \item "ind": label only active individuals.
-#' \item "var": label only active variables.
-#' \item "none": no labels.
+#' \item "all": Label both active individuals and active variables.
+#' \item "ind": Label only active individuals.
+#' \item "var": Label only active variables.
+#' \item "none": No labels.
 #' }
 #' 
 #' @param show_percentage A boolean (default = TRUE) specifying whether to show the

diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
diff --git a/docs/articles/index.html b/docs/articles/index.html
diff --git a/docs/articles/scaffold.html b/docs/articles/scaffold.html
diff --git a/docs/articles/usage_template.html b/docs/articles/usage_template.html
diff --git a/docs/authors.html b/docs/authors.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -4,7 +4,7 @@ pkgdown_sha: ~
 articles:
   scaffold: scaffold.html
   usage_template: usage_template.html
-last_built: 2024-07-06T22:46Z
+last_built: 2024-07-07T04:18Z
 urls:
   reference: https://uconn-scs.github.io/msDiaLogue/reference
   article: https://uconn-scs.github.io/msDiaLogue/articles