Usage
champ.process(fromIDAT = TRUE, fromFile = FALSE, directory = getwd(), resultsDir =
paste(getwd(), "resultsChamp", sep = "/"), methValue = "B", filterDetP = TRUE,
detPcut = 0.01, filterXY = TRUE, removeDetP = 0, filterBeads = TRUE, beadCutoff =
0.05, filterNoCG = FALSE, QCimages = TRUE, batchCorrect = TRUE, runSVD =
TRUE, studyInfo = FALSE, infoFactor = c(), norm = "BMIQ", adjust.method = "BH",
adjPVal = 0.05, runDMR = TRUE, runCNA = TRUE, plotBMIQ = FALSE, DMRpval = 0.05,
sampleCNA=TRUE,plotSample = TRUE,groupFreqPlots=TRUE,freqThreshold=0.3, bedFile
= FALSE, methProfile = FALSE, controlProfile = FALSE,arraytype="450K")
Arguments
fromIDAT
If fromIDAT=TRUE, data is imported from .idat files with an associated sample sheet (.csv). If rawdata=FALSE then data is uploaded from a text file (saved as "beta.txt". Default is TRUE.)
directory
The directory where the .idat files and sample sheet are located, default is current working directory.
resultsDir
Directory where results will be saved. Default is to create a folder called "resultsChamp"in the current working directory.
methValue
Indicates whether you prefer the methylation scores to be calculated as m-values (M) or beta-values (B). Default is B.
filterDetP
If filter=TRUE, probes that have a detection p-value below detPcut are filtered out. Default is TRUE.
detPcut
If filter=TRUE, this value with be used as the significance threshold for filtering out probes based on the detection p-value. Default=0.01.
filterXY
If filterXY=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.
removeDetP
The removeDetP parameter represents the fraction of samples that can contain a detection p-value above the detPcut. Default is 0.
filterBeads
If filterBeads=TRUE, probes with a beadcount less than 3 will be removed depending on the beadCutoff value. Default is TRUE.
beadCutoff
The beadCutoff represents the fraction of samples that must have a beadcount less than 3 before the probe is removed. Default is 0.05 or 5 percent of samples.
filterNoCG
If filterNoCG=TRUE, non-cg probes are removed. Default is FALSE.
batchCorrect
If batchCorrect=TRUE, then the ComBat batch correction will be performed on batch effects related to bead chip. Default is TRUE.
runSVD
If runSVD=TRUE, SVD analysis for identifying batch effects will be performed. Default is TRUE.
studyInfo
If runSVD = TRUE, additional study covariate information can be included in the SVD analysis. Default is FALSE.
norm
This specifies which normalization method will be used. Values can be BMIQ (by default), PBC, SWAN or NONE.
adjPVal
The minimum threshold of significance for probes to be includede in DMRs, default = 0.05
adjust.method
The p-value adjustment method to be used for the limma analyis, default= BH (Bonferroni-Hochberg)
runDMR
If runDMR=TRUE, runs the probe lasso method for finding DMRs. This will result in an MVP list with p-values and a DMR list with p-values. Default is TRUE.
runCNA
If runCNA=TRUE, copy number abberation analysis will be performed. Default is TRUE.
plotBMIQ
If plotBMIQ=TRUE and norm="BMIQ", BMIQ plots will be saved. Default is TRUE.
DMRpval
If runDMR=TRUE, this value will be used as the cutoff for the DMR p-value. Default is 0.05.
sampleCNA
If sampleCNA=TRUE, then . Default is TRUE.
plotSample
If plotSample=TRUE, CNA plots will be saved. Default is TRUE.
groupFreqPlots
If groupFreqPlots=T, then
freqThreshold
If groupFreqPlots=T, then freqThreshold will be used as the cutoff for calling a gain or loss. Default is 0.03.
bedFile
if bedFile = TRUE. MVP list will be saved as an additional file in bedfile format for downstream analysis. Defaults is TRUE.
methProfile
If methProfile=TRUE then the beta values will be uploaded using the MethylationProbeProfile file from Genome Studio. Default is FALSE.
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.
arraytype
Choose microarray type is 450K or EPIC.