library(TCGAutils)
devtools::load_all("~/Documents/github/TCGAutils")
brcaList <-
list.files("~/Documents/github/MultiAssayExperiment-TCGA/data/raw/BRCA",
full.names = TRUE)
brcaNames <- vapply(strsplit(basename(brcaList), "_"), `[`, character(1L), 2)
brcaNames <- vapply(strsplit(brcaNames, "-"), `[`, character(1L), 1)
names(brcaList) <- brcaNames
brcaList <- brcaList[ -which(names(brcaList) == "Methylation")]
## TEST
brcaList <- brcaList[3L]
brcaActual <- brcaList
names(brcaActual) <- basename(brcaList)
brcaActual <- lapply(brcaActual, readRDS)
mergeIdxBRCA <- lapply(seq_along(brcaActual), function(i, dataTab) {
type <- strsplit(names(dataTab[i]), "_|-")
type <- vapply(type, function(x) { x[[2L]] }, character(1L))
dataObject <- .removeShell(dataTab[[i]], type)
if (is.list(dataObject) && !is.data.frame(dataObject)) {
dataList <- .unNestList(dataObject)
if (length(dataList) > 1L) {
compareDF <- .compareListElements(dataList)
TCGAutils:::.getMergeIndices(compareDF)
} else { return(NULL) }
} else { return(NULL) }
}, dataTab = brcaActual)
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