ExperimentList {MultiAssayExperiment} | R Documentation |
ExperimentList
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)