usageExample.R

In miccec/CPTACBiolinks: What the Package Does (One Line, Title Case)

library(devtools)
install_github("miccec/CPTACBiolinks")
library(CPTACBiolinks)

## GET DATASETS LIST
getDatasetsList()

## GET DATA LIST OF CANCER
CancerType = "Endometrial"
getOmicsList(CancerType)

## GET ALL DATASETS OF AN OMICS TYPE FROM CANCER
# Possible options: 
# "Clinical","SCNV","Mutation","Acetylproteome","Phosphoproteome","Proteome"        
# "RNAseq","miRNA","Circular","Methylation","CNV","Glycoproteome","RPPA" 
OmicsType = "Phosphoproteome"
phosphopro = getDataType(CancerType,OmicsType)
names(phosphopro)

## GET SPECIFIC DATA OF CANCER
DataType = "Phosphoproteome (Gene level, Tumor)"
phosphopro = getData(CancerType,DataType)
head(phosphopro)

## GET MULTI DATA OF CANCER
DataType = c("RNAseq (HiSeq, Gene level, Tumor)", "Proteome (Gene level, TMT Unshared Log Ratio, Tumor)")
endometrial_omics = getData(CancerType,DataType)
names(endometrial_omics)

## GET ALL DATA OF CANCER
all_endometrial = getData(CancerType,"All")
names(all_endometrial)

## TOP n MUTATED GENES
Mutation = all_endometrial$`Mutation (Gene level, Tumor)`
topMutatedGene(Mutation, 10)


## SUBSET RNAseq MATRIX ONLY PATIENT WITH GENE MUTATION
RNAseq = all_endometrial$`RNAseq (HiSeq, Gene level, Tumor)`
Mutation = all_endometrial$`Mutation (Gene level, Tumor)`
gene = topMutatedGene(Mutation, 1)

RNAseq_sub = subsetSharedMutation(RNAseq,Mutation,gene$geneID)

# PLOT MUTATIONS
plotMutations(Mutation)