QuackenbushLab · katehoffshutta · May 7, 2025 · May 7, 2025
diff --git a/.gitignore b/.gitignore
@@ -4,4 +4,7 @@
 *#
 .Rproj.user
 testdata/*
-*testthat-problems.rds
+*testthat-problems.rds
+.DS_Store
+/doc/
+/Meta/
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,21 +1,21 @@
 Package: NetworkDataCompanion
 Title: Tools for Analyzing TCGA and GTEx Data
-Version: 0.0.0.9000
+Version: 0.1.0
 Authors@R: 
-    c(person("Soel", "Micheletti", email = "smicheletti@hsph.harvard.edu", role = c("aut", "cre"),
-           comment = c(ORCID = "0000-0001-5402-9237")),
-    person("Chen", "Chen",
-                        email = "cchen22@hsph.harva",role = "aut", comment = c(ORCID = "0000-0002-8042-7201")),
-    person("Kate", "Shutta",
-                        email = "kshutta@hsph.harvard.edu",role = "aut", comment = c(ORCID = "0000-0003-0402-3771")),
-    person("Panagiotis", "Mandros", email = "pmandros@hsph.harvard.edu", role = c("aut", "cre"),
+    c(person("Chen", "Chen", email = "chenchen9945@gmail.com",role = "aut", 
+     comment = c(ORCID = "0000-0002-8042-7201")),
+    person("Panagiotis", "Mandros", email = "mandros.p@gmail.com", role = c("aut"),
            comment = c(ORCID = "0009-0008-9638-9722")),
-    person("Viola", "Fanfani", email = "vfanfani@hsph.harvard.edu", role = c("aut", "cre"),
+    person("Viola", "Fanfani", email = "vfanfani@hsph.harvard.edu", role = c("aut"),
            comment = c(ORCID = "0000-0003-3852-6908")),
-    person("Jonas", "Fischer", email = "jfischer@hsph.harvard.edu", role = c("aut", "cre"),
-           comment = c(ORCID = "0000-0000-0000-0000")))
-Author: Kate Hoff Shutta <kshutta@hsph.harvard.edu>, Viola Fanfani <vfanfani@hsph.harvard.edu>, Soel Micheletti <smicheletti@hsph.harvard.edu>, Panagiotis Mandros <pmandros@hsph.harvard.edu>, Jonas Fischer <jfischer@hsph.harvard.edu>, Chen Chen <cchen22@hsph.harvard.edu>
-Maintainer: Kate Hoff Shutta <kshutta@hsph.harvard.edu>
+    person("Jonas", "Fischer", email = "jonas.fischer@mpi-inf.mpg.de", role = c("aut"),
+           comment = c(ORCID = "0000-0002-6459-5053")),
+    person("Panagiotis", "Mandros", email = "mandros.p@gmail.com", role = c("aut"),
+           comment = c(ORCID = "0009-0008-9638-9722")),
+    person("Soel", "Micheletti", email = "smicheletti@hsph.harvard.edu", role = c("aut"),
+           comment = c(ORCID = "0000-0001-5402-9237")),
+    person("Kate Hoff", "Shutta",  email = "kshutta@hsph.harvard.edu",role = c("aut","cre"), 
+      comment = c(ORCID = "0000-0003-0402-3771")))
 Description: An R library of utilities for performing analyses on TCGA and GTEx data using the Network Zoo (https://netzoo.github.io).
 License: GPL-3
 biocViews:

diff --git a/NetworkDataCompanion.pdf b/NetworkDataCompanion.pdf
diff --git a/R/NetworkDataCompanion.R b/R/NetworkDataCompanion.R
@@ -17,18 +17,17 @@
 #' @field sample_type_mapping A `data.frame` for sample type classification and mapping.
 #'
 #' @section Methods:
-#' Placeholder for methods documentation. Define each method here once methods are added.
 #'
 #' @references
 #' https://www.biorxiv.org/content/10.1101/2024.11.05.622163v1.abstract
 #'
 #' @author
+#' Chen Chen (\email{chenchen9945@gmail.com}),
 #' Viola Fanfani (\email{vfanfani@hsph.harvard.edu}),
-#' Jonas Fischer (\email{jfischer@hsph.harvard.edu}),
-#' Panagiotis Mandros (\email{pmandros@hsph.harvard.edu}),
+#' Jonas Fischer (\email{jonas.fischer@mpi-inf.mpg.de}),
+#' Panagiotis Mandros (\email{mandros.p@gmail.com}),
 #' Soel Micheletti (\email{smicheletti@hsph.harvard.edu}),
 #' Kate Hoff Shutta (\email{kshutta@hsph.harvard.edu})
-#'
 #' @export NetworkDataCompanion
 NetworkDataCompanion=setRefClass("NetworkDataCompanion",
 

diff --git a/man/CreateNetworkDataCompanionObject.Rd b/man/CreateNetworkDataCompanionObject.Rd
@@ -20,6 +20,6 @@ CreateNetworkDataCompanionObject(clinical_patient_file, project_name)
 }
 
 \author{
-Panagiotis Mandros (pmandros@hsph.harvard.edu)
+Panagiotis Mandros
 
 }
diff --git a/man/NetworkDataCompanion-class.Rd b/man/NetworkDataCompanion-class.Rd
diff --git a/man/convertBetaToM.Rd b/man/convertBetaToM.Rd
@@ -22,5 +22,5 @@ A numeric vector of m-values corresponding to the converted values of \code{meth
 \url{https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-587}
 }
 \author{
-Kate Hoff Shutta (kshutta@hsph.harvard.edu)
+Kate Hoff Shutta 
 }
diff --git a/man/estimateCellCountsEpiSCORE.Rd b/man/estimateCellCountsEpiSCORE.Rd
@@ -23,5 +23,5 @@ Teschendorff, A.E., Zhu, T., Breeze, C.E. et al. EPISCORE: cell type deconvoluti
 }
 
 \author{
-Kate Hoff Shutta (kshutta@hsph.harvard.edu)
+Kate Hoff Shutta 
 }
diff --git a/man/extractSampleAndGeneInfo.Rd b/man/extractSampleAndGeneInfo.Rd
@@ -24,7 +24,7 @@ Extracts experiment-specific information and metadata from ranged summarized exp
 \item{rds_gene_info}{metadata about the genes (rows)}
 }
 \author{
-Jonas Fischer (jfischer@hsph.harvard.edu)
+Jonas Fischer 
 }
 
 %% ~Make other sections like Warning with \section{Warning }{....} ~
diff --git a/man/filterBarcodesIntersection.Rd b/man/filterBarcodesIntersection.Rd
@@ -25,6 +25,6 @@ No additional details at this time.
 }
 
 \author{
-Jonas Fischer (jfischer@hsph.harvard.edu)
+Jonas Fischer
 }
 
diff --git a/man/filterChromosome.Rd b/man/filterChromosome.Rd
@@ -20,5 +20,5 @@ This function filters for genes in a particular chromosome or chromosomes.
 }
 
 \author{
-Jonas Fischer (jfischer@hsph.harvard.edu)
+Jonas Fischer 
 }
diff --git a/man/filterDuplicatesSeqDepth.Rd b/man/filterDuplicatesSeqDepth.Rd
@@ -19,5 +19,5 @@ This function filters out duplicates based on RNA-seq, keeping the samples with
 }
 
 \author{
-Jonas Fischer(jfischer@hsph.harvard.edu)
+Jonas Fischer
 }
diff --git a/man/filterDuplicatesSeqDepthOther.Rd b/man/filterDuplicatesSeqDepthOther.Rd
diff --git a/man/filterGenesByTPM.Rd b/man/filterGenesByTPM.Rd
@@ -19,5 +19,5 @@ Filter all genes which have at least \code{tpm_threshold} TPM scores in at least
 \value{Integer vector indexing the rows of \code{expression_tpm_matrix} that correspond to genes that should be kept.}
 
 \author{
-Jonas Fischer (jfischer@hsph.harvard.edu)
+Jonas Fischer 
 }
diff --git a/man/filterGenesProteins.Rd b/man/filterGenesProteins.Rd
@@ -18,5 +18,5 @@ Filtering protein coding genes through an rds object.
 }
 
 \author{
-Jonas Fischer (jfischer@hsph.harvard.edu)
+Jonas Fischer 
 }
diff --git a/man/filterPurity.Rd b/man/filterPurity.Rd
@@ -27,6 +27,6 @@ Integer vector of indices indicating which samples in \code{TCGA_barcodes} shoul
 This code is based on the \code{TCGAPurityFiltering} package found at \url{https://github.com/pmandros/TCGAPurityFiltering}.}
 
 \author{
-Panagiotis Mandros (pmandros@hsph.harvard.edu)
+Panagiotis Mandros 
 }
 
diff --git a/man/filterSampleType.Rd b/man/filterSampleType.Rd
@@ -23,5 +23,5 @@
 }
 
 \author{
-  Jonas Fischer (jfischer@hsph.harvard.edu)
+  Jonas Fischer
 }
diff --git a/man/filterTumorType.Rd b/man/filterTumorType.Rd
@@ -23,5 +23,5 @@ Candidate values for \code{type_of_tumor}: "Primary Tumor", "Solid Tissue Normal
 }
 
 \author{
-Jonas Fischer (jfischer@hsph.harvard.edu)
+Jonas Fischer
 }
diff --git a/man/geneNameToENSG.Rd b/man/geneNameToENSG.Rd
@@ -21,5 +21,5 @@ Convert from gene name to Ensembl stable id.
 \url{https://useast.ensembl.org/index.html}
 }
 \author{
-Panagiotis Mandros (pmandros@hsph.harvard.edu)}
+Panagiotis Mandros}
 
diff --git a/man/getGeneInfo.Rd b/man/getGeneInfo.Rd
@@ -22,6 +22,6 @@ A data frame with rows representing genes and columns representing gene attribut
 }
 
 \author{
-Panagiotis Mandros (pmandros@hsph.harvard.edu)
+Panagiotis Mandros 
 }
 
diff --git a/man/logCPMNormalization.Rd b/man/logCPMNormalization.Rd
@@ -19,7 +19,7 @@ This function computes CPM values from raw expression counts using the edgeR pac
 \item{logCPM}{log(CPM + 1) transformed values of the same shape as the count matrix.}
 }
 \author{
-Jonas Fischer (jfischer@hsph.harvard.edu)
+Jonas Fischer
 }
 \references{
 \url{https://bioconductor.org/packages/release/bioc/html/edgeR.html}

diff --git a/man/logTPMNormalization.Rd b/man/logTPMNormalization.Rd
@@ -25,6 +25,6 @@ and the actual log TPM. A pseudocount of 1 is added to each TPM value for this f
 RangedSummarizedExperiment documentation
 }
 \author{
-Jonas Fischer (jfischer@hsph.harvard.edu)
+Jonas Fischer
 }
 
diff --git a/man/mapBarcodeToBarcode.Rd b/man/mapBarcodeToBarcode.Rd
@@ -27,7 +27,7 @@ The same information is provided for \code{bc2}.
 \item{idcs2}{Integer vector of the same length as \code{bc2} that indicates where to find each barcode of \code{bc2} in \code{bc1}, returning \code{NA} if there is no match. That is, \code{idcs2[i] != NA}, then \code{bc2[i] == bc1[idcs2[i]]}.}
 }
 \author{
-Jonas Fischer (jfischer@hsph.harvard.edu)
+Jonas Fischer 
 }
 \note{For example, if you want to map experiment 1 onto experiment 2, keeping only the information for samples that are present in both, and reordering the first experiment to match the samples of the second, you can do:
 

diff --git a/man/mapProbesToGenes.Rd b/man/mapProbesToGenes.Rd
@@ -25,7 +25,7 @@ https://zwdzwd.github.io/InfiniumAnnotation
 }
 \author{
 %%  ~~who you are~~
-Kate Hoff Shutta (kshutta@hsph.harvard.edu)
+Kate Hoff Shutta 
 }
 
 %% ~Make other sections like Warning with \section{Warning }{....} ~
diff --git a/man/probeToMeanPromoterMethylation.Rd b/man/probeToMeanPromoterMethylation.Rd
@@ -17,5 +17,5 @@
 }
 
 \author{
-Kate Hoff Shutta (kshutta@hsph.harvard.edu)
+Kate Hoff Shutta
 }