obtainMultipleStudies: Obtain the requested data for various cancer studies.

In cbaf: Automated functions for comparing various omic data from cbioportal.org

Description

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.

Usage

obtainMultipleStudies(genesList, submissionName, studiesNames,
  desiredTechnique, cancerCode = FALSE, validateGenes = TRUE)

Arguments

genesList	a list that contains at least one gene group
submissionName	a character string containing name of interest. It is used for naming the process.
studiesNames	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 "Acute Myeloid Leukemia (TCGA, NEJM 2013)". Alternatively, a matrix can used if users prefer user-defined cancer names. In this case, the first column of matrix comprises the standard cancer names while the second column must contain the desired cancer names.
desiredTechnique	a character string that is one of the following techniques: "RNA-Seq", "microRNA-Seq", "microarray.mRNA" , "microarray.microRNA" or "methylation".
cancerCode	a logical value that tells the function to use cbioportal abbreviated cancer names instead of complete cancer names, if set to be TRUE. For example, "laml_tcga_pub" is the abbreviated name for "Acute Myeloid Leukemia (TCGA, NEJM 2013)".
validateGenes	a logical value that, if set to be TRUE, function will check each cancer study to find whether or not each gene has a record. If a cancer study doesn't have a record for specific gene, it checks for alternative gene names that cbioportal might use instead of the given gene name.

Details

Package:	cbaf
Type:	Package
Version:	1.12.1
Date:	2020-12-07
License:	Artistic-2.0

Value

a BiocFileCach object that contains the obtained data without further processing. Name of the object is combination of bfc_ and 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. Additonally, if validateGenes = TRUE, another section that contains gene validation results will be created in the BiocFileCach object.

Author(s)

Arman Shahrisa, [e-mail] [maintainer, copyright holder]

Maryam Tahmasebi Birgani, [e-mail]

Examples

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")

cbaf documentation built on Dec. 9, 2020, 2:02 a.m.