normalizeWithinSamples {charm} | R Documentation |
Within-sample (between-channel) normalization for two-color DNA methylation microarray data. This function implements the control probe loess procedure described in Aryee et al., 2011 (PMID: 20858772).
normalizeWithinSamples(dat, copy=TRUE, method = "loess", scale=c(0.99, 0.99), controlProbes = NULL, controlIndex = NULL, approx=TRUE, breaks=1000, verbose=FALSE)
dat |
a TilingFeatureSet |
copy |
Only relevant when using disk-backed objects. If TRUE a copy will be made leaving the original object (dat) unchanged. The input object will not be preserved if copy=FALSE |
method |
normalization method. "loess" or "none" |
scale |
a numeric vector (x,y). The xth percentile of each sample is scaled to represent y% methylation. The default c(0.99, 0.99) means probes in the 99% percentile represent 99% methylation. Set to NA for no scaling. |
controlProbes |
character string of the label assigned to non-CpG control probes in the annotation file (i.e. the container column of the .ndf file). |
controlIndex |
a vector of non-CpG control probe indices |
approx |
Bin probes by signal intensity when loess normalizing. Much faster when TRUE |
breaks |
Number of bins to use when approx=TRUE |
verbose |
boolean: Verbose output? |
This function is used by methp
performs within-sample (between-channel) normalization. It is normally not used directly by the user.
a TilingFeatureSet
Martin Aryee <aryee@jhu.edu>, Rafael Irizarry
# See normalizeBetweenSamples