funCV: funCV

In simulatorZ: Simulator for Collections of Independent Genomic Data Sets

Description

Cross validation function

Usage

funCV(obj, fold, y.var, trainFun = masomenos, funCvSubset = cvSubsets, 


    covar = NULL)

Arguments

obj	a ExpressionSet, matrix or RangedSummarizedExperiment object. If it is a matrix, columns represent samples
fold	the number of folds in cross validation
y.var	response variable, matrix, data.frame(with 2 columns) or Surv object
trainFun	training function, which takes gene expression matrix X and response variable y as input, the coefficients as output
funCvSubset	function to divide one Expression Set into subsets for cross validation
covar	other covariates to be added in as predictors

Value

returns the c statistics of cross validation(CV)

Author(s)

Yuqing Zhang, Christoph Bernau, Levi Waldron

Examples

library(curatedOvarianData)


library(GenomicRanges)


set.seed(8)


data( E.MTAB.386_eset )


eset <- E.MTAB.386_eset[1:100, 1:30]


rm(E.MTAB.386_eset)





time <- eset$days_to_death


cens.chr <- eset$vital_status


cens <- rep(0, length(cens.chr))


cens[cens.chr=="living"] <- 1


y <- Surv(time, cens)  


y1 <- cbind(time, cens)





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 <- c(1588,1929,1813,1542,1830,1775)  


cens <- c(1,0,1,1,1,1)


y.vars <- Surv(time, cens)





funCV(eset, 3, y)


funCV(exprs(eset), 3, y1)


funCV(sset, 3, y.vars)


## any training function will do as long as it takes the gene expression matrix X


## and response variable y(matrix, data.frame or Surv object) as parameters, and


## return the coefficients as its value

simulatorZ documentation built on Nov. 8, 2020, 5 p.m.