slSummarization {cn.farms} | R Documentation |
The different probes of the SNPs of the array are summarized to a probeset.
slSummarization(object, summaryMethod = "Exact", summaryParam = list(), callParam = list(runtype = "ff", cores = 1), summaryWindow = c("std", "fragment"), returnValues, saveFile = "slData")
object |
An instance of
|
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. |
summaryWindow |
Method for combination of the SNPs. Possible values are sl and fragment. |
returnValues |
List with return values. |
saveFile |
Name of the file to save. |
Single-locus summarized data of an instance of
ExpressionSet
Djork-Arne Clevert okko@clevert.de and Andreas Mitterecker mitterecker@bioinf.jku.at
load(system.file("exampleData/normData.RData", package = "cn.farms")) notes(experimentData(normData))$annotDir <- system.file("exampleData/annotation/pd.genomewidesnp.6/1.1.0", package = "cn.farms") summaryMethod <- "Variational" summaryParam <- list() summaryParam$cyc <- c(10) slData <- slSummarization(normData, summaryMethod = summaryMethod, summaryParam = summaryParam) assayData(slData)$L_z[1:10, 1:10] summaryMethod <- "Gaussian" summaryParam <- list() summaryParam$cyc <- c(10) slData <- slSummarization(normData, summaryMethod = summaryMethod, summaryParam = summaryParam) assayData(slData)$L_z[1:10, 1:10] summaryMethod <- "Exact" summaryParam <- list() summaryParam$cyc <- c(10, 20) slData <- slSummarization(normData, summaryMethod = summaryMethod, summaryParam = summaryParam) assayData(slData)$L_z[1:10, 1:10]