ExperimentList {MultiAssayExperiment} | R Documentation |
ExperimentList
object for the MultiAssayExperiment
object slot.The ExperimentList
class can contain several different types of data.
The only requirements for an ExperimentList
class are that the
objects contained have the following set of methods: dim
, [
,
dimnames
ExperimentList(...)
... |
A named |
A ExperimentList
class object of experiment data
## Create an empty ExperimentList instance ExperimentList() ## Create array matrix and AnnotatedDataFrame to create an ExpressionSet class arraydat <- matrix(data = seq(101, length.out = 20), ncol = 4, dimnames = list( c("ENST00000294241", "ENST00000355076", "ENST00000383706","ENST00000234812", "ENST00000383323"), c("array1", "array2", "array3", "array4") )) colDat <- data.frame(slope53 = rnorm(4), row.names = c("array1", "array2", "array3", "array4")) ## SummarizedExperiment constructor exprdat <- SummarizedExperiment::SummarizedExperiment(arraydat, colData = colDat) ## Create a sample methylation dataset methyldat <- matrix(data = seq(1, length.out = 25), ncol = 5, dimnames = list( c("ENST00000355076", "ENST00000383706", "ENST00000383323", "ENST00000234812", "ENST00000294241"), c("methyl1", "methyl2", "methyl3", "methyl4", "methyl5") )) ## Create a sample RNASeqGene dataset rnadat <- matrix( data = sample(c(46851, 5, 19, 13, 2197, 507, 84318, 126, 17, 21, 23979, 614), size = 20, replace = TRUE), ncol = 4, dimnames = list( c("XIST", "RPS4Y1", "KDM5D", "ENST00000383323", "ENST00000234812"), c("samparray1", "samparray2", "samparray3", "samparray4") )) ## Create a mock RangedSummarizedExperiment from a data.frame rangedat <- data.frame(chr="chr2", start = 11:15, end = 12:16, strand = c("+", "-", "+", "*", "."), samp0 = c(0,0,1,1,1), samp1 = c(1,0,1,0,1), samp2 = c(0,1,0,1,0), row.names = c(paste0("ENST", "00000", 135411:135414), "ENST00000383323")) rangeSE <- SummarizedExperiment::makeSummarizedExperimentFromDataFrame(rangedat) ## Combine to a named list and call the ExperimentList constructor function assayList <- list(Affy = exprdat, Methyl450k = methyldat, RNASeqGene = rnadat, GISTIC = rangeSE) ## Use the ExperimentList constructor ExpList <- ExperimentList(assayList)