vignettes/useCase.md

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

useCase

Get multi omics data of Endometrial

library(CPTACBiolinks)
CancerType = "Endometrial"
proteomics = getDataType(CancerType,"Proteome")

## [1] "Loading Proteome"

RNAseq = getDataType(CancerType,"RNAseq")

## [1] "Loading RNAseq"

mutation = getDataType(CancerType,"mutation")

## [1] "Loading mutation"
## -Reading
## -Validating
## -Summarizing
## -Processing clinical data
## --Missing clinical data
## -Finished in 4.122s elapsed (19.0s cpu)

Plot Mutation

plotMutations(mutation$`Mutation (Gene level, Tumor)`)
plotMutations(mutation$`Mutation (Site level, Tumor)`)

Subset RNAseq and Proteomics with shared mutation

RNAseq_tum = RNAseq$`RNAseq (HiSeq, Gene level, Tumor)`
proteomics_tum = proteomics$`Proteome (Gene level, TMT Unshared Log Ratio, Tumor)`
mutation_tum = mutation$`Mutation (Gene level, Tumor)`

top_gene = topMutatedGenes(mutation_tum, 1)

RNAseq_sub = subsetSharedMutation(RNAseq_tum,mutation_tum,top_gene$geneID)
proteomics_sub = subsetSharedMutation(proteomics_tum,mutation_tum,top_gene$geneID)

Boxplot EGFR RNAseq and Proteomics

samples_notPTEN <- colnames(proteomics_tum)[!colnames(proteomics_tum) %in% colnames(proteomics_sub)]

boxplot(list(PTEN_MUT = t(proteomics_sub["EGFR",]), PTEN_WT = t(proteomics_tum["EGFR",samples_notPTEN])), main ="EGFR (proteomics)")

boxplot(list(PTEN_MUT = t(RNAseq_sub["EGFR",]), PTEN_WT = t(RNAseq_tum["EGFR",samples_notPTEN])), main ="EGFR (RNAseq)")

miccec/CPTACBiolinks documentation built on Dec. 21, 2021, 5:56 p.m.