MultiAssayExperiment from vignette

myMultiAssay.R

library(Biobase)
library(MultiAssayExperiment)
patient.data <- data.frame(sex=c("M", "F", "M", "F"),
                           age=38:41,
                           row.names=c("Jack", "Jill", "Bob", "Barbara"))
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)

## ------------------------------------------------------------------------
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)

## ------------------------------------------------------------------------
suppressPackageStartupMessages(library(GenomicRanges))
## completely encompasses ENST00000355076
gr1 <-
  GRanges(seqnames = "chr3", ranges = IRanges(58000000, 59502360),
          strand = "+", score = 5L, GC = 0.45)
## first is within ENST0000035076
gr2 <-
  GRanges(seqnames = c("chr3", "chr3"),
          ranges = IRanges(c(58493000, 3), width=9000),
          strand = c("+", "-"), score = 3:4, GC = c(0.3, 0.5))
gr3 <-
  GRanges(seqnames = c("chr1", "chr2"),
          ranges = IRanges(c(1, 4), c(3, 9)),
          strand = c("-", "-"), score = c(6L, 2L), GC = c(0.4, 0.1))
grl <- GRangesList("gr1" = gr1, "gr2" = gr2, "gr3" = gr3)
names(grl) <- c("snparray1", "snparray2", "snparray3")
grl

## ------------------------------------------------------------------------
rangemap <- data.frame(primary = c("Jack", "Jill", "Jill"),
                        assay = c("snparray1", "snparray2", "snparray3"),
                        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)

## ------------------------------------------------------------------------
rangemap2 <-
   data.frame(primary = c("Jack", "Jill", "Bob", "Barbara"),
              assay = c("mysnparray1", "mysnparray2", "mysnparray3",
                        "mysnparray4"), stringsAsFactors = FALSE)

## ------------------------------------------------------------------------
listmap <- list(exprmap, methylmap, micromap, rangemap, rangemap2)
names(listmap) <- c("Affy", "Methyl 450k", "Mirna", "CNV gistic", "CNV gistic2")

## ------------------------------------------------------------------------
dfmap <- listToMap(listmap)

## ---- eval=FALSE---------------------------------------------------------
## mapToList(dfmap, "assay")

## ------------------------------------------------------------------------
objlist <- list("Affy" = exprdat, "Methyl 450k" = methyldat,
                "Mirna" = microdat, "CNV gistic" = grl, "CNV gistic2" = rse)

## ------------------------------------------------------------------------
myMultiAssay <- MultiAssayExperiment(objlist, patient.data, dfmap)