gdcClinicalMerge: Merge clinical data

In Jialab-UCR/GDCRNATools: GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, mRNA, and miRNA data in GDC

Description

Merge clinical data in .xml files that are downloaded from GDC to a dataframe

Usage

gdcClinicalMerge(path, key.info = TRUE, organized = FALSE)

Arguments

path	path to downloaded files for merging
key.info	logical, whether to return the key clinical information only. If TRUE, only clinical information such as age, stage, grade, overall survial, etc. will be returned
organized	logical, whether the clinical data have already been organized into a single folder (eg., data downloaded by the 'GenomicDataCommons' method are already organized). Default is FALSE.

Value

A dataframe of clinical data with rows are patients and columns are clinical traits

Author(s)

Ruidong Li and Han Qu

Examples

####### Merge clinical data #######
path <- 'Clinical/'
## Not run: clinicalDa <- gdcClinicalMerge(path=path, key.info=TRUE)

Jialab-UCR/GDCRNATools documentation built on Nov. 28, 2020, 11:23 a.m.