Description Usage Arguments Details Value Author(s) Examples
View source: R/cbaf-obtainMultipleStudies.R
This function Obtains the requested data for the given genes across multiple cancer studies. It can check whether or not all genes are included in cancer studies and, if not, looks for the alternative gene names.
obtainMultipleStudies(genesList, submissionName, studiesNames, desiredTechnique, cancerCode = FALSE, validateGenes = TRUE)
a list that contains at least one gene group
a character string containing name of interest. It is used for naming the process.
a character vector or a matrix that containes desired
cancer names. The character vector containes standard
names of cancer studies that can be found on cbioportal.org, such as
a character string that is one of the following
a logical value that tells the function to use cbioportal
abbreviated cancer names instead of complete cancer names, if set to be
a logical value that, if set to be
a BiocFileCach object that contains the obtained data without further
processing. Name of the object is combination of
submissionName. Inside it, there is a section for the obtained data,
which is stored as a list. At first level, this list is subdivided into
diferent groups based on the list of genes that user has given the function,
then each gene group itself contains one matrix for every cancer study.
validateGenes = TRUE, another section that contains
gene validation results will be created in the BiocFileCach object.
Arman Shahrisa, email@example.com [maintainer, copyright holder]
Maryam Tahmasebi Birgani, firstname.lastname@example.org
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genes <- list(K.demethylases = c("KDM1A", "KDM1B", "KDM2A", "KDM2B", "KDM3A", "KDM3B", "JMJD1C", "KDM4A"), K.methyltransferases = c("SUV39H1", "SUV39H2", "EHMT1", "EHMT2", "SETDB1", "SETDB2", "KMT2A", "KMT2A")) studies <- c("Acute Myeloid Leukemia (TCGA, Provisional)", "Adrenocortical Carcinoma (TCGA, Provisional)", "Bladder Urothelial Carcinoma (TCGA, Provisional)", "Brain Lower Grade Glioma (TCGA, Provisional)", "Breast Invasive Carcinoma (TCGA, Provisional)") obtainMultipleStudies(genes, "test2", studies, "RNA-Seq")
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