## ---- echo=FALSE, warning=FALSE-------------------------------------------- suppressPackageStartupMessages({ library(MultiAssayExperiment) library(GenomicRanges) }) ## ---- eval = FALSE--------------------------------------------------------- # source("https://bioconductor.org/biocLite.R") # BiocInstaller::biocLite("MultiAssayExperiment") ## ---- eval = FALSE--------------------------------------------------------- # library(MultiAssayExperiment) # library(GenomicRanges) ## -------------------------------------------------------------------------- empty <- MultiAssayExperiment() empty slotNames(empty) ## -------------------------------------------------------------------------- class(experiments(empty)) # ExperimentList ## -------------------------------------------------------------------------- patient.data <- data.frame(sex=c("M", "F", "M", "F"), age=38:41, row.names=c("Jack", "Jill", "Bob", "Barbara")) patient.data ## -------------------------------------------------------------------------- class(sampleMap(empty)) # DataFrame ## -------------------------------------------------------------------------- exprss1 <- matrix(rnorm(16), ncol = 4, dimnames = list(sprintf("ENST00000%i", sample(288754:290000, 4)), c("Jack", "Jill", "Bob", "Bobby"))) exprss2 <- matrix(rnorm(12), ncol = 3, dimnames = list(sprintf("ENST00000%i", sample(288754:290000, 4)), c("Jack", "Jane", "Bob"))) doubleExp <- list("methyl 2k" = exprss1, "methyl 3k" = exprss2) simpleMultiAssay <- MultiAssayExperiment(experiments=doubleExp) simpleMultiAssay ## -------------------------------------------------------------------------- colData(simpleMultiAssay) ## -------------------------------------------------------------------------- simpleMultiAssay2 <- MultiAssayExperiment(experiments=doubleExp, colData=patient.data) simpleMultiAssay2 colData(simpleMultiAssay2) ## -------------------------------------------------------------------------- class(metadata(empty)) # NULL (class "ANY") ## ---- message=FALSE-------------------------------------------------------- library(Biobase) (arraydat <- matrix(seq(101, 108), ncol=4, dimnames=list(c("ENST00000294241", "ENST00000355076"), c("array1", "array2", "array3", "array4")))) arraypdat <- as(data.frame(slope53=rnorm(4), row.names=c("array1", "array2", "array3", "array4")), "AnnotatedDataFrame") exprdat <- ExpressionSet(assayData=arraydat, phenoData=arraypdat) exprdat ## -------------------------------------------------------------------------- (exprmap <- data.frame(primary=rownames(patient.data)[c(1, 2, 4, 3)], assay=c("array1", "array2", "array3", "array4"), stringsAsFactors = FALSE)) ## -------------------------------------------------------------------------- (methyldat <- matrix(1:10, ncol=5, dimnames=list(c("ENST00000355076", "ENST00000383706"), c("methyl1", "methyl2", "methyl3", "methyl4", "methyl5")))) ## -------------------------------------------------------------------------- (methylmap <- data.frame(primary = c("Jack", "Jack", "Jill", "Barbara", "Bob"), assay = c("methyl1", "methyl2", "methyl3", "methyl4", "methyl5"), stringsAsFactors = FALSE)) ## -------------------------------------------------------------------------- (microdat <- matrix(201:212, ncol=3, dimnames=list(c("hsa-miR-21", "hsa-miR-191", "hsa-miR-148a", "hsa-miR148b"), c("micro1", "micro2", "micro3")))) ## -------------------------------------------------------------------------- (micromap <- data.frame(primary = c("Jack", "Barbara", "Bob"), assay = c("micro1", "micro2", "micro3"), stringsAsFactors = FALSE)) ## -------------------------------------------------------------------------- library(SummarizedExperiment) nrows <- 5; ncols <- 4 counts <- matrix(runif(nrows * ncols, 1, 1e4), nrows) rowRanges <- GRanges(rep(c("chr1", "chr2"), c(2, nrows - 2)), IRanges(floor(runif(nrows, 1e5, 1e6)), width=100), strand=sample(c("+", "-"), nrows, TRUE), feature_id=sprintf("ID\\%03d", 1:nrows)) names(rowRanges) <- letters[1:5] colData <- DataFrame(Treatment=rep(c("ChIP", "Input"), 2), row.names= c("mysnparray1", "mysnparray2", "mysnparray3", "mysnparray4")) rse <- SummarizedExperiment(assays=SimpleList(counts=counts), rowRanges=rowRanges, colData=colData) ## -------------------------------------------------------------------------- (rangemap <- data.frame(primary = c("Jack", "Jill", "Bob", "Barbara"), assay = c("mysnparray1", "mysnparray2", "mysnparray3", "mysnparray4"), stringsAsFactors = FALSE)) ## -------------------------------------------------------------------------- listmap <- list(exprmap, methylmap, micromap, rangemap) names(listmap) <- c("Affy", "Methyl 450k", "Mirna", "CNV gistic") listmap ## -------------------------------------------------------------------------- dfmap <- listToMap(listmap) dfmap ## ---- eval=FALSE----------------------------------------------------------- # mapToList(dfmap, "assay") ## -------------------------------------------------------------------------- objlist <- list("Affy" = exprdat, "Methyl 450k" = methyldat, "Mirna" = microdat, "CNV gistic" = rse) ## -------------------------------------------------------------------------- myMultiAssay <- MultiAssayExperiment(objlist, patient.data, dfmap) myMultiAssay ## -------------------------------------------------------------------------- experiments(myMultiAssay) colData(myMultiAssay) sampleMap(myMultiAssay) metadata(myMultiAssay) ## -------------------------------------------------------------------------- objlist3 <- objlist (names(objlist3) <- NULL) try(prepMultiAssay(objlist3, patient.data, dfmap)$experiments) ## -------------------------------------------------------------------------- names(objlist3) <- toupper(names(objlist)) names(objlist3) unique(dfmap[, "assay"]) prepMultiAssay(objlist3, patient.data, dfmap)$experiments ## -------------------------------------------------------------------------- exampleMap <- sampleMap(simpleMultiAssay2) sapply(doubleExp, colnames) exampleMap prepMultiAssay(doubleExp, patient.data, exampleMap)$metadata$drops ## -------------------------------------------------------------------------- exMap <- rbind(dfmap, DataFrame(assay = "New methyl", primary = "Joe", colname = "Joe")) invisible(prepMultiAssay(objlist, patient.data, exMap)) ## -------------------------------------------------------------------------- prepped <- prepMultiAssay(objlist, patient.data, exMap) preppedMulti <- MultiAssayExperiment(prepped$experiments, prepped$colData, prepped$sampleMap, prepped$metadata) preppedMulti ## -------------------------------------------------------------------------- do.call(MultiAssayExperiment, prepped) ## -------------------------------------------------------------------------- library(GenomicRanges) grlls <- list(chr = rep("chr1", nrows), start = seq(11, 15), end = seq(12, 16), strand = c("+", "-", "+", "*", "*"), score = seq(1, 5), specimen = c("a", "a", "b", "b", "c"), gene_symbols = paste0("GENE", letters[seq_len(nrows)])) grldf <- as.data.frame(grlls, stringsAsFactors = FALSE) makeGRangesListFromDataFrame(grldf, split.field = "specimen", names.field = "gene_symbols") ## -------------------------------------------------------------------------- library(SummarizedExperiment) sels <- list(chr = rep("chr2", nrows), start = seq(11, 15), end = seq(12, 16), strand = c("+", "-", "+", "*", "*"), expr0 = seq(3, 7), expr1 = seq(8, 12), expr2 = seq(12, 16)) sedf <- as.data.frame(sels, row.names = paste0("GENE", letters[rev(seq_len(nrows))]), stringsAsFactors = FALSE) sedf makeSummarizedExperimentFromDataFrame(sedf) ## ---- eval=FALSE----------------------------------------------------------- # myMultiAssay[rows, columns, assays] ## -------------------------------------------------------------------------- myMultiAssay["ENST00000355076", , ] ## -------------------------------------------------------------------------- myMultiAssay["ENST00000355076", 1:2, c("Affy", "Methyl 450k")] ## -------------------------------------------------------------------------- myMultiAssay[, "Jack", ] myMultiAssay[, 1, ] myMultiAssay[, c(TRUE, FALSE, FALSE, FALSE), ] ## -------------------------------------------------------------------------- myMultiAssay[, , "Mirna"] myMultiAssay[, , 3] myMultiAssay[, , c(FALSE, FALSE, TRUE, FALSE, FALSE)] ## -------------------------------------------------------------------------- myMultiAssay["ENST00000355076", , , drop=FALSE] ## -------------------------------------------------------------------------- myMultiAssay["ENST00000355076", , , drop=TRUE] ## -------------------------------------------------------------------------- colData(myMultiAssay) ## -------------------------------------------------------------------------- myMultiAssay[, 1:2] ## -------------------------------------------------------------------------- malesMultiAssay <- myMultiAssay[, myMultiAssay$sex == "M"] colData(malesMultiAssay) ## -------------------------------------------------------------------------- allsamples <- colnames(myMultiAssay) allsamples ## -------------------------------------------------------------------------- allsamples[["Methyl 450k"]] <- allsamples[["Methyl 450k"]][-3:-5] myMultiAssay[, as.list(allsamples), ] subsetByColumn(myMultiAssay, as.list(allsamples)) #equivalent ## -------------------------------------------------------------------------- myMultiAssay[, , c("Affy", "CNV gistic")] ## -------------------------------------------------------------------------- is.cnv = grepl("CNV", names(experiments(myMultiAssay))) is.cnv myMultiAssay[, , is.cnv] #logical subsetting myMultiAssay[, , which(is.cnv)] #integer subsetting ## -------------------------------------------------------------------------- featSubsetted0 <- subsetByRow(myMultiAssay, "ENST00000355076") featSubsetted0 <- myMultiAssay["ENST00000355076", , ] #equivalent class(featSubsetted0) class(experiments(featSubsetted0)) experiments(featSubsetted0) ## -------------------------------------------------------------------------- featSubsetted <- subsetByRow(myMultiAssay, c("ENST00000355076", "ENST00000294241")) exprs(experiments(myMultiAssay)[[1]]) exprs(experiments(featSubsetted)[[1]]) ## -------------------------------------------------------------------------- gr <- GRanges(seqnames = c("chr1", "chr1", "chr2"), strand = c("+", "+", "+"), ranges = IRanges(start = c(330602, 443625, 934533), end = c(330701, 443724, 934632))) ## -------------------------------------------------------------------------- subsetted <- subsetByRow(myMultiAssay, gr, maxgap = 2L, type = "within") experiments(subsetted) rowRanges(subsetted[[4]]) ## -------------------------------------------------------------------------- names(myMultiAssay) myMultiAssay[[1]] myMultiAssay[["Affy"]] ## -------------------------------------------------------------------------- colData(myMultiAssay) ## -------------------------------------------------------------------------- complete.cases(myMultiAssay) ## -------------------------------------------------------------------------- complete.cases(myMultiAssay[, , 1:2]) ## -------------------------------------------------------------------------- myMultiAssay[, complete.cases(myMultiAssay), ] ## -------------------------------------------------------------------------- duplicated(myMultiAssay) ## -------------------------------------------------------------------------- (noMatches <- intersectRows(myMultiAssay)) ## -------------------------------------------------------------------------- complete.cases(myMultiAssay) colData(myMultiAssay)[complete.cases(myMultiAssay), ] ## -------------------------------------------------------------------------- intersectColumns(myMultiAssay) ## -------------------------------------------------------------------------- duplicated(myMultiAssay) ## -------------------------------------------------------------------------- mergeReplicates(intersectColumns(myMultiAssay)) ## -------------------------------------------------------------------------- longFormat(myMultiAssay[, , 1:2]) ## -------------------------------------------------------------------------- longFormat(myMultiAssay[, , 1:2], colDataCols="age") ## -------------------------------------------------------------------------- maemerge <- mergeReplicates(intersectColumns(myMultiAssay)) wideFormat(maemerge, shape="wide", colDataCols="sex")[, 1:5] ## -------------------------------------------------------------------------- assay(myMultiAssay) ## -------------------------------------------------------------------------- assays(myMultiAssay) ## -------------------------------------------------------------------------- rownames(myMultiAssay) colnames(myMultiAssay) ## -------------------------------------------------------------------------- objlist2 <- objlist objlist2[[2]] <- as.vector(objlist2[[2]]) invalid.obj <- try(MultiAssayExperiment(objlist2, patient.data, dfmap)) invalid.obj ## ---- eval=FALSE----------------------------------------------------------- # API() ## ---- eval=FALSE----------------------------------------------------------- # API(shiny=TRUE) ## -------------------------------------------------------------------------- methods(class="MultiAssayExperiment") ## -------------------------------------------------------------------------- sessionInfo()