mlSummarization {cn.farms} | R Documentation |
Method for computation of the multi-loci summarization
mlSummarization(object, windowMethod, windowParam, summaryMethod, summaryParam, callParam = list(runtype = "ff"), returnValues, saveFile = "mlData")
object |
an instance of |
windowMethod |
Method for combination of neighbouring SNPs. Possible values are Std and Bps. |
windowParam |
further parameters as the window size |
summaryMethod |
allowed versions for the summarization step are: Gaussian, Variational, Exact. Default is Variational. |
summaryParam |
The parameters for the summaryMethod. Further information
can be obtained via the according functions:
|
callParam |
Additional parameters for runtype (ff or bm) as well as cores for parallelization. |
returnValues |
List with return values. |
saveFile |
Name of the file to save. For possible values see summaryMethod. |
Multi-loci summarized data of an instance of
ExpressionSet
Djork-Arne Clevert okko@clevert.de and Andreas Mitterecker mitterecker@bioinf.jku.at
load(system.file("exampleData/slData.RData", package = "cn.farms")) windowMethod <- "std" windowParam <- list() windowParam$windowSize <- 5 windowParam$overlap <- TRUE summaryMethod <- "Variational" summaryParam <- list() summaryParam$cyc <- c(20) mlData <- mlSummarization(slData, windowMethod, windowParam, summaryMethod, summaryParam) assayData(mlData)