Usage
champ.SVD(beta = myNorm$beta, rgSet = myLoad$rgSet, detP = myLoad$detP, pd = myLoad$pd,
loadFile = FALSE, betaFile = "beta.txt", sampleSheet = "sampleSheet.txt", methProfile = FALSE,
methFile = "MethylationProbeProfile.txt", controlProfile = FALSE,
controlFile = "ControlProbeProfile.txt", studyInfo = FALSE, studyInfoFile = "studyInfo.txt",
infoFactor = c(), resultsDir = paste(getwd(), "resultsChamp", sep = "/"))
Arguments
beta
A matrix of values representing the methylation scores for each sample (M or B). The default assumes you ran champ.norm and saved the output to "myNorm".
rgSet
An rgSet object that was created when data was loaded the data from the .idat files. The default assumes you ran champ.load and saved the output to "myLoad".
detP
A matrix of detection p-values for each sample. The default assumes you ran champ.load and saved the output to "myLoad".
pd
This data.frame includes the information from the sample sheet. The default assumes you ran champ.load and saved the output to "myLoad".
loadFile
If loadFile=TRUE, then the beta values and sample sheet need to be uploaded
sampleSheet
If the data has not been loaded from .idat files and fromFile=TRUE then this points to the required sampleSheet. Default is "sampleSheet.txt"
methProfile
If methprofile=TRUE then the beta values will be uploaded using the MethylationProbeProfile file from Genome Studio
methFile
If methProfile=TRUE then the beta values will be uploaded using the MethylationProbeProfile from Genome Studio. This is the name of the file. Default is "MethylationProbeProfile.txt"
controlProfile
If rawdata = FALSE and runSVD = TRUE, then it is useful to have a control probe profile file exported from Genome Studio so that internal control probes can be included in the SVD analyis. Default is FALSE.
controlFile
If controlProfile = TRUE then the control probe values will be uploaded using the ControlProbeProfile from Genome Studio. This is the name of the file. Default is "ControlProbeProfile.txt"
studyInfo
If studyInfo=TRUE, additional study covariate information can be included in the SVD analysis. Default is FALSE.
studyInfoFile
If studyInfo =T, this file will include the additional study information. Default is "studyInfo.txt".
resultsDir
Directory where results will be saved. Default is to create a folder called "resultsChamp"in the current working directory.