diff --git a/.gitignore b/.gitignore index 65b91bd..e72d55d 100644 --- a/.gitignore +++ b/.gitignore @@ -4,4 +4,7 @@ *# .Rproj.user testdata/* -*testthat-problems.rds \ No newline at end of file +*testthat-problems.rds +.DS_Store +/doc/ +/Meta/ diff --git a/DESCRIPTION b/DESCRIPTION index 5e79fd5..ba33b6b 100644 --- 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 , Viola Fanfani , Soel Micheletti , Panagiotis Mandros , Jonas Fischer , Chen Chen -Maintainer: Kate Hoff Shutta + 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 new file mode 100644 index 0000000..82f0454 Binary files /dev/null and b/NetworkDataCompanion.pdf differ diff --git a/R/NetworkDataCompanion.R b/R/NetworkDataCompanion.R index dfa8340..6b6809d 100644 --- 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 index 47c302c..20b77f8 100644 --- 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 } \ No newline at end of file diff --git a/man/NetworkDataCompanion-class.Rd b/man/NetworkDataCompanion-class.Rd index e2561d9..ed9fa02 100644 --- a/man/NetworkDataCompanion-class.Rd +++ b/man/NetworkDataCompanion-class.Rd @@ -29,16 +29,16 @@ A package for easy and reproducible wrangling of TCGA and GTEx data. \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}) } diff --git a/man/convertBetaToM.Rd b/man/convertBetaToM.Rd index db03476..6cabc14 100644 --- 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 index e071ee5..76a0dcd 100644 --- 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 index e6523ff..3f37b6b 100644 --- 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 index f4f6049..5009675 100644 --- 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 index 0e2b6df..87a19f9 100644 --- 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 index f8fd201..535abd9 100644 --- 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 deleted file mode 100644 index 49f35b3..0000000 --- a/man/filterDuplicatesSeqDepthOther.Rd +++ /dev/null @@ -1,26 +0,0 @@ -\name{filterDuplicatesSeqDepthOther} -\alias{\S4method{filterDuplicatesSeqDepthOther}{NetworkDataCompanion}} -%- Also NEED an '\alias' for EACH other topic documented here. -\title{A version of \code{filterDuplicatesSeqDepth} to handle the case when sequencing depth is not available. -} -\description{ -This function takes a random duplicate if no info is available on sequencing depth for all vials. -} - -\usage{ -\S4method{filterDuplicatesSeqDepthOther}{NetworkDataCompanion}(expression_count_matrix, tcga_barcodes) -} -%- maybe also 'usage' for other objects documented here. -\arguments{ - \item{expression_count_matrix}{Matrix of count data from RNA-seq experiment, with genes in rows and samples in columns.} - \item{tcga_barcodes}{List of TCGA barcodes for filtering.} -%% ~~Describe \code{x} here~~ -} - -\value{ -Integer vector of indices to KEEP in \code{tcga_barcodes}. -} - -\author{ -Jonas Fischer (jfischer@hsph.harvard.edu) -} diff --git a/man/filterGenesByTPM.Rd b/man/filterGenesByTPM.Rd index d85de45..2a060b1 100644 --- 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 index 25203f6..8b875e7 100644 --- 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 index 60c6878..6b49903 100644 --- 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 index f472eb1..d17699a 100644 --- 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 index 92d4b0c..85af697 100644 --- 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 index 6efd7bc..03e0dd9 100644 --- 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 index 68ec355..f4e7b76 100644 --- 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 index 261f828..9417adb 100644 --- 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 index 54f48ae..20a2b1d 100644 --- 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 index 0bc7118..c5a6511 100644 --- 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 index 47579fe..25a5c5b 100644 --- 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 index 56eaafe..5bfd612 100644 --- a/man/probeToMeanPromoterMethylation.Rd +++ b/man/probeToMeanPromoterMethylation.Rd @@ -17,5 +17,5 @@ } \author{ -Kate Hoff Shutta (kshutta@hsph.harvard.edu) +Kate Hoff Shutta }