obtainOneStudy: Obtain the requested data for various subgroups of a cancer...

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

Obtain the requested data for various subgroups of a cancer study.

Description

This function Obtains the requested data for the given genes across multiple subgroups of a cancer. It can check whether or not all genes are included in subgroups of a cancer study and, if not, looks for the alternative gene names.

Usage

obtainOneStudy(genesList, submissionName, studyName, desiredTechnique,
  desiredCaseList = 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.
studyName	a character string showing the desired cancer name. It is an standard cancer study name that can be found on cbioportal.org, such as "Acute Myeloid Leukemia (TCGA, NEJM 2013)".
desiredTechnique	a character string that is one of the following techniques: "RNA-Seq", "RNA-SeqRTN", "microRNA-Seq", "microarray.mRNA", "microarray.microRNA" or "methylation".
desiredCaseList	a numeric vector that contains the index of desired cancer subgroups, assuming the user knows index of desired subgroups. If not, desiredCaseList is set to "none", function will show the available subgroups and ask the user to enter the desired ones during the process. The default value is "none".
validateGenes	a logical value that, if set to be 'TRUE', causes the function to check each cancer study to find whether or not each gene has a record. If a cancer doesn't have a record for specific gene, function looks for alternative gene names that cbioportal might use instead of the given gene name.

Details

Package:	cbaf
Type:	Package
Version:	1.19.5
Date:	2022-07-19
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 study subgroup. 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"))

obtainOneStudy(genes, "test", "Breast Invasive Carcinoma (TCGA, Cell 2015)",
"RNA-Seq", desiredCaseList = c(2,3,4,5))

armanshahrisa/cbaf documentation built on Nov. 5, 2022, 3:21 a.m.