Usage
champ.norm(beta = myLoad$beta, rgSet = myLoad$rgSet, pd = myLoad$pd, mset = myLoad$mset,
sampleSheet = "sampleSheet.txt", resultsDir = paste(getwd(), "resultsChamp",
sep = "/"), methValue = "B", fromIDAT = TRUE, norm = "BMIQ", fromFile = FALSE, betaFile,
filter = TRUE, filterXY = TRUE, QCimages = FALSE, plotBMIQ = FALSE,arraytype="450K")
Arguments
arraytype
Choose microarray type is 450K or EPIC.
beta
A matrix of values representing the methylation scores for each sample (M or B). The default assumes you ran champ.load and saved the output to "myLoad".
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".
pd
This data.frame includes the information from the sample sheet. The default assumes you ran champ.load and saved the output to "myLoad".
mset
Loads an mset object that was created when data was loaded from the .idat files. The default assumes you ran champ.load and saved the output to "myLoad".
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".
resultsDir
Directory where results will be saved. Default is a folder in the current working directory called "resultsChamp".
methValue
Indicates whether you prefer the methylation scores to be calculated as m-values (M) or beta-values (B). Default is B.
norm
This specifies which normalization method will be used. Values can be BMIQ (by default), PBC, SWAN or NONE.
fromFile
If loadFile=TRUE, then the beta values and sample sheet need to be uploaded.
filter
Not yet implemented. If fromFile=T and this is from a genome studio file, probes that have a detection p-value below detPcut are filtered out. Default is TRUE.
filterXY
If fromFile=True, probes from X and Y chromosomes are removed. Default is TRUE.
QCimages
If QCimages=TRUE, then quality control images are saved to the resultsDir. Default is TRUE.
plotBMIQ
If plotBMIQ=TRUE and norm="BMIQ", BMIQ plots will be saved. Default is TRUE.