dmrFinder:
Find differentially methylated regions (DMRs)
Description
Find differentially methylated regions (DMRs) from tiling microarray data. If you want to adjust for covariates (including batch effects estimated using SVA) or if your covariate of interest is continuous, use the dmrFind function.
Usage
dmrFinder(eset=NULL, groups, p=NULL, l=NULL, chr=NULL, pos=NULL, pns=NULL,
sdBins=NULL, controlIndex=NULL, controlProbes=NULL, Indexes=NULL,
filter=NULL, package=NULL, ws=7, verbose=TRUE, compare="all",
withinSampleNorm="loess", betweenSampleNorm="quantile",
cutoff=0.995, sortBy="ttarea", removeIf=expression(nprobes<3), paired="FALSE," pairs="NULL," dd="NULL," comps="NULL," comps.names="NULL)
3),>
Arguments
groups
a vector of group labels for the samples in eset
p
a matrix of percentage methylation values (scale: 0, 1). One column per sample
l
a matrix of methylation values (scale: -Inf, Inf), typically log-ratios.
chr
vector of chromosome labels for the probes in eset, p or l
pos
vector of chromosomal coordinates for the probes in eset, p or l
pns
vector of region names for the probes in eset, p or l
sdBins
not currently implemented
controlIndex
vector of indices of non-CpG control probes (which can be obtained using getControlIndex), to be passed on to the methp function if neither the p nor the l arguments are provided, in which case either this or the controlProbes argument must be provided.
controlProbes
names of probe containers corresponding to control probes (e.g., see values returned by getContainer), to be passed on to the methp function if neither the p nor the l arguments are provided, in which case either this or the controlIndex argument must be provided.
Indexes
not currently used
filter
smoothing window weights. See details
package
annotation package name
ws
smoothing window size parameter. See details.
verbose
Verbose progress reporting
compare
the groups between which to find DMRs.
withinSampleNorm
within-sample normalization method. "loess" or "none"
betweenSampleNorm
between-sample normalization method. "quantile", "sqn" or "none"
cutoff
t-statistic cutoff used to identify probes as being in a DMR
sortBy
sort column for the DMR table. "area", "ttarea", "avg.diff", or "max.diff".
removeIf
expression indicating which DMRs to drop from the DMR tables that get returned. The negation of this is used as the subset argument to the subset function when it is called on the final DMR table before it is returned. If NULL, no DMRs will be subsetted out from the final table before it is returned. DMR table column names to use are listed below. E.g., to drop all DMRs with less than 4 probes, set removeIf=expression(nprobes
paired
if TRUE, do comparisons within pairs of samples. FALSE by default.
pairs
if paired=TRUE, this must be provided. a vector of pair identifiers for the samples in eset. values must be the same within pairs and different between pairs.
COMPS
Ignore this argument.
COMPS.names
Ignore this argument.