zmatrix {simulatorZ}R Documentation

zmatrix

Description

generate a matrix of c statistics

Usage

zmatrix(obj, y.vars, fold, trainingFun = masomenos, cvFun = funCV, 
    cvSubsetFun = cvSubsets)

Arguments

obj

a list of ExpressionSet, matrix or RangedSummarizedExperiment objects. If its elements are matrices, columns represent samples

y.vars

a list of response variables, all the response variables shold be matrix, data.frame(with 2 columns) or Surv object

fold

cvFun parameter, in this case passes to funCV()

trainingFun

training function

cvFun

function to perform cross study within one set

cvSubsetFun

function to divide the expression sets into subsets for cross validation

Value

outputs one matrix of validation statistics

Author(s)

Yuqing Zhang, Christoph Bernau, Levi Waldron

Examples

library(curatedOvarianData)
library(GenomicRanges)
data(GSE17260_eset)
data(E.MTAB.386_eset)
data(GSE14764_eset)
esets <- list(GSE17260=GSE17260_eset, E.MTAB.386=E.MTAB.386_eset, GSE14764=GSE14764_eset)
esets.list <- lapply(esets, function(eset){
  return(eset[1:500, 1:20])
})

## simulate on multiple ExpressionSets
set.seed(8) 

y.list <- lapply(esets.list, function(eset){
  time <- eset$days_to_death
  cens.chr <- eset$vital_status
  cens <- c()
  for(i in seq_along(cens.chr)){
    if(cens.chr[i] == "living") cens[i] <- 1
    else cens[i] <- 0
  }
  y <- Surv(time, cens)
  return(y)
})

# generate on original ExpressionSets
z <- zmatrix(esets.list, y.list, 3)

# generate on simulated ExpressionSets
simmodels <- simBootstrap(esets.list, y.list, 10, 100)
z <- zmatrix(simmodels$obj.list, simmodels$y.vars.list, 3)

# support matrix
X.list <- lapply(esets.list, function(eset){
  newx <- exprs(eset) ### columns represent samples !!
  return(newx)
}) 
z <- zmatrix(X.list, y.list, 3)

# support RangedSummarizedExperiment
nrows <- 200; ncols <- 6
counts <- matrix(runif(nrows * ncols, 1, 1e4), nrows)
rowRanges <- GRanges(rep(c("chr1", "chr2"), c(50, 150)),
                     IRanges(floor(runif(200, 1e5, 1e6)), width=100),
                     strand=sample(c("+", "-"), 200, TRUE))
colData <- DataFrame(Treatment=rep(c("ChIP", "Input"), 3),
                     row.names=LETTERS[1:6])
sset <- SummarizedExperiment(assays=SimpleList(counts=counts),
                             rowRanges=rowRanges, colData=colData)

time <- sample(4500:4700, 6, replace=TRUE)
cens <- sample(0:1, 6, replace=TRUE)
y.vars <- Surv(time, cens)

z <- zmatrix(list(sset[,1:3], sset[,4:6]), list(y.vars[1:3,],y.vars[4:6,]), 3)

[Package simulatorZ version 1.14.0 Index]