inst/doc/QuickStartMultiAssay.R

In MultiAssayExperiment: Software for the integration of multi-omics experiments in Bioconductor

## ----include=TRUE,results="hide",message=FALSE,warning=FALSE------------------
library(MultiAssayExperiment)
library(S4Vectors)

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data(miniACC)
miniACC

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colData(miniACC)[1:4, 1:4]
table(miniACC$race)

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experiments(miniACC)

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sampleMap(miniACC)

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metadata(miniACC)

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miniACC[c("MAPK14", "IGFBP2"), , ]

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miniACC[, miniACC$pathologic_stage == "stage iv", ]

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miniACC[, , "RNASeq2GeneNorm"]

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miniACC[[1L]]  #or equivalently, miniACC[["RNASeq2GeneNorm"]]

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summary(complete.cases(miniACC))

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accmatched = intersectColumns(miniACC)

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colnames(accmatched)

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accmatched2 <- intersectRows(miniACC[, , c("RNASeq2GeneNorm",
                                           "gistict",
                                           "Mutations")])
rownames(accmatched2)

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class(assay(miniACC))

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assays(miniACC)

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longFormat(miniACC[c("TP53", "CTNNB1"), , ],
           colDataCols = c("vital_status", "days_to_death"))

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wideFormat(miniACC[c("TP53", "CTNNB1"), , ],
           colDataCols = c("vital_status", "days_to_death"))

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MultiAssayExperiment(experiments=experiments(miniACC),
    colData=colData(miniACC),
    sampleMap=sampleMap(miniACC),
    metadata=metadata(miniACC))

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miniACC2 <- c(miniACC, log2rnaseq = log2(assays(miniACC)$RNASeq2GeneNorm), mapFrom=1L)
assays(miniACC2)

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library(UpSetR)
upsetSamples(miniACC)

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suppressPackageStartupMessages({
  library(survival)
  library(survminer)
})
coldat <- as.data.frame(colData(miniACC))
coldat$y <- Surv(miniACC$days_to_death, miniACC$vital_status)
colData(miniACC) <- DataFrame(coldat)

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miniACC <- miniACC[, complete.cases(coldat$y), ]
coldat <- as(colData(miniACC), "data.frame")

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fit <- survfit(y ~ pathology_N_stage, data = coldat)
ggsurvplot(fit, data = coldat, risk.table = TRUE)

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wideacc <- wideFormat(miniACC["EZH2", , ],
    colDataCols = c("vital_status", "days_to_death", "pathology_N_stage"))
wideacc$y <- Surv(wideacc$days_to_death, wideacc$vital_status)
head(wideacc)

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coxph(Surv(days_to_death, vital_status) ~ gistict_EZH2 +
          log2(RNASeq2GeneNorm_EZH2) + pathology_N_stage,  data=wideacc)

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sessionInfo()