rmSNPandCH(object, dist = 2, mafcut = 0.05, and = TRUE, rmcrosshyb = TRUE, rmXY=FALSE)TRUE, the probe must have at least 1 SNP binding to it
that satisfies both requirements in dist and
mafcut for it to be filtered out. If FALSE, it will be
filtered out if either requirement is satisfied. Default is
TRUE.
TRUE, filters out probes found by Chen et al. (2013) to be
cross-reactive with areas of the genome not at the site of
interest. Many of these sites are on the X-chromosome, leading to
potential confounding if the sample group is a mix of males and
females. There are 30,969 probes in total in this list. Default is
TRUE.
TRUE, filters out probe hybridising to sex chromosomes. Or-operator applies when combined with other 2 filters.
object, with rows corresponding to
probes matching user input filtered out.
-1:dist will be filtered out for any integer
specification of dist. When a probe is listed as being ``-1''
nucleotides from a SNP (7 in total of the 153,113), that SNP is
immediately adjacent to the end of the probe, and is likely to
confound the measurement, in addition to those listed as 0, 1 or 2
nucleotides away. See vignette for further details.
## Not run:
# data(dmrcatedata)
# myMs <- logit2(myBetas)
# myMs.noSNPs <- rmSNPandCH(myMs, dist=2, mafcut=0.05)
# ## End(Not run)
Run the code above in your browser using DataLab