Usage
champ.load(directory = getwd(), methValue = "B", resultsDir = paste(getwd(), "resultsChamp", sep = "/"), filterXY = TRUE, QCimages = TRUE, filterDetP = TRUE, detPcut = 0.01, removeDetP = 0, filterBeads=TRUE, beadCutoff=0.05, filterNoCG=FALSE,filterSNPs=TRUE,filterMultiHit=TRUE,arraytype="450K")
Arguments
arraytype
Choose microarray type is 450K or EPIC.
directory
Location of IDAT files, default is current working directory.
methValue
Indicates whether you prefer m-values M or beta-values B.
resultsDir
Directory where results will be saved.
QCimages
If QCimages=T, then images will be saved.
filterDetP
If filter = T, then probes above the detPcut will be filtered out.
filterXY
If filterXY=TRUE, probes from X and Y chromosomes are removed. Default is TRUE.
detPcut
The detection p-value threshhold. Probes about this cutoff will be filtered out. Default is 0.01
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% of samples.
filterNoCG
If filterNoCG=TRUE, non-cg probes are removed. Default is FALSE.
filterSNPs
If filterSNPs=TRUE, probes in which the probed CpG falls near a SNP as defined in Nordlund et al are removed. Default is TRUE.
filterMultiHit
If filterMultiHit=TRUE, probes in which the probe aligns to multiple locations with bwa as defined in Nordlund et al are removed.. Default is TRUE.