### *GDCRNATools* - an R/Bioconductor package for downloading, organizing, and integrative analyzing lncRNA, mRNA, and miRNA data in GDC * **The [GDCRNATools Manual](http://bioconductor.org/packages/devel/bioc/vignettes/GDCRNATools/inst/doc/GDCRNATools.html) and R code of the [GDCRNATools Workflow](https://github.com/Jialab-UCR/Jialab-UCR.github.io/blob/master/GDCRNATools.workflow.R) has been updated in 10-30-2018.** * **If you use `GDCRNATools` in your published research, please cite:** Li, R., Qu, H., Wang, S., Wei, J., Zhang, L., Ma, R., Lu, J., Zhu, J., Zhong, W., and Jia, Z. (2018). GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, miRNA and mRNA data in GDC. Bioinformatics 34, 2515-2517. https://doi.org/10.1093/bioinformatics/bty124. * **Please add my WeChat: rli012 or email to rli012@ucr.edu if you have further questions.** *** ## 1. Introduction The [Genomic Data Commons (GDC)](https://portal.gdc.cancer.gov/) maintains standardized genomic, clinical, and biospecimen data from National Cancer Institute (NCI) programs including [The Cancer Genome Atlas (TCGA)](https://tcga-data.nci.nih.gov/) and [Therapeutically Applicable Research To Generate Effective Treatments (TARGET)](https://ocg.cancer.gov/programs/target), It also accepts high quality datasets from non-NCI supported cancer research programs, such as genomic data from the [Foundation Medicine](https://www.foundationmedicine.com/). `GDCRNATools` is an R/Bioconductor package which provides a standard, easy-to-use and comprehensive pipeline for downloading, organizing, and integrative analyzing RNA expression data in the GDC portal with an emphasis on deciphering the lncRNA-mRNA related ceRNA regulatory network in cancer. ## 2. Manual and R script (updated in 10-30-2018) The comprehensive manual of `GDCRNATools` is available here: [GDCRNATools Manual](http://bioconductor.org/packages/devel/bioc/vignettes/GDCRNATools/inst/doc/GDCRNATools.html) R code of the workflow is available here: [GDCRNATools Workflow](https://github.com/Jialab-UCR/Jialab-UCR.github.io/blob/master/GDCRNATools.workflow.R) ## 3. Installation ### 3.1 Installation via Bioconductor * The stable release version of [`GDCRNATools`](https://bioconductor.org/packages/release/bioc/html/GDCRNATools.html) requires R(>=3.5.0) and Bioconductor(>=3.8). Please start R and enter: ```R ## try http:// if https:// URLs are not supported if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager") BiocManager::install("GDCRNATools") ``` * To install the development version of [`GDCRNATools`](https://bioconductor.org/packages/devel/bioc/html/GDCRNATools.html), please update your R and Biocondutor to the latest version and run: ```R if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager") BiocManager::install("GDCRNATools", version = "devel") ``` ### 3.2 Installation locally Please download the compressed package here: [GDCRNATools_1.1.5.tar.gz](https://github.com/Jialab-UCR/Jialab-UCR.github.io/blob/master/GDCRNATools_1.1.5.tar.gz) #### 3.2.1 On Windows system * Make sure that your R is installed in 'c:\program files' * Install [Rtools](https://cran.r-project.org/bin/windows/Rtools/) in 'c:\program files' * Add R and Rtools to the Path Variable on the Environment Variables panel, including c:\program files\Rtools\bin c:\program files\Rtools\gcc-4.6.3\bin c:\program files\R\R.3.x.x\bin\i386 c:\program files\R\R.3.x.x\bin\x64 * Run the following code in R ```R install.packages('GDCRNATools_1.1.5.tar.gz', repos = NULL, type='source') ``` #### 3.2.2 On Linux and Mac systems Just run the following code in R ```R install.packages('GDCRNATools_1.1.5.tar.gz', repos = NULL, type='source') ``` ### 3.3 Note If `GDCRNATools` cannot be installed due to the lack of dependencies, please run the following code ahead to install those pacakges either simutaneously or separately: ```R if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager") ### install packages simutaneously ### BiocManager::install(c('limma', 'edgeR', 'DESeq2', 'clusterProfiler', 'DOSE', 'org.Hs.eg.db', 'biomaRt', 'BiocParallel', 'GenomicDataCommons')) install.packages(c('shiny', 'jsonlite', 'rjson', 'survival', 'survminer', 'ggplot2', 'gplots', 'Hmisc', 'DT', 'matrixStats', 'xml2')) ### install packages seperately ### BiocManager::install('limma') BiocManager::install('edgeR') BiocManager::install('DESeq2') BiocManager::install('clusterProfiler') BiocManager::install('DOSE') BiocManager::install('org.Hs.eg.db') BiocManager::install('biomaRt') BiocManager::install('BiocParallel') BiocManager::install('GenomicDataCommons') install.packages('shiny') install.packages('jsonlite') install.packages('rjson') install.packages('survival') install.packages('survminer') install.packages('ggplot2') install.packages('gplots') install.packages('Hmisc') install.packages('DT') install.packages('matrixStats') install.packages('xml2') ``` ## 4. Frequently Asked Questions. **Q1: gdcRNADownload() function doesn't work with the following error:** Error in FUN(X[[i]], ...): unused arguments(desination_dir=directory, overwrite=TRUE) **A1:** This error occurs when the default API method for downloading fails. Please add `method='gdc-client'` to the gdcRNADownload() function. ```R ####### Download RNAseq data ####### project <- 'TCGA-CHOL' rnadir <- paste(project, 'RNAseq', sep='/') gdcRNADownload(project.id = 'TCGA-CHOL', data.type = 'RNAseq', write.manifest = FALSE, method = 'gdc-client', ### use 'gdc-client' to download data directory = rnadir) ``` **Q2: gdcRNAMerge() doesn't work with the following error:** Error in open.connection(file, 'rt'): cannot open the connection In addition: Warning message: In open.connection(file, 'rt'): cannot open compressed file 'TCGA-XXXX/RNAseq/xxx-xxx-xxx-xxx.htseq.counts.gz', probable reason 'No such file or directory'. **A2:** This is usually because the data for different samples are downloaded in separate folders. Please add `organized=FALSE` to the gdcRNAMerge() function. ```R ####### Merge RNAseq data ####### rnaCounts <- gdcRNAMerge(metadata = metaMatrix.RNA, path = rnadir, organized = FALSE, # if the data are in separate folders data.type = 'RNAseq') ```