xlsxOutput: Generate excel output for various studies/subgroups of a...

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

Generate excel output for various studies/subgroups of a study.

Description

This function generates excel files containing gene validation and all selected statistical methods. It uses outputs of obtainOneStudy()/obtainMultipleStudies() and automatedStatistics() functions.

Usage

xlsxOutput(submissionName, transposeResults = FALSE)

Arguments

submissionName	a character string containing name of interest. It is used for naming the process.
transposeResults	a logical value that enables the function to replace the columns and rows of data.

Details

Package:	cbaf
Type:	Package
Version:	1.19.5
Date:	2022-07-19
License:	Artistic-2.0

Value

It generates one excel file for each gene group. This excel file contains output of automatedStatistics() and validation result from output of either obtainOneStudy() or obtainMultipleStudies().

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(3,4))

automatedStatistics("test", obtainedDataType = "single study", calculate =
c("frequencyPercentage", "frequencyRatio"))

xlsxOutput("test")

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