BayMethList | R Documentation |
"BayMethList"
This S4 class captures the genomic windows together with the number of read counts obtained by affinity-enrichment sequencing experiments for a fully methylated control and one or more samples of interest. Furthermore CpG-density is stored.
Creates a BayMethList object:
BayMethList(windows, control, sampleInterest, cpgDens,
f=matrix(), priorTab=list(), methEst=list(), maskEmpBayes=logical())
windows
A GRanges
object.
control
A matrix of read counts obtained by an
affinity enrichment sequencing experiment for the fully
methylated (SssI) treated sample. The number of rows must be
equal to length(windows)
. Each column contains the
counts of one sample. The number of columns must be either one
or equal to the number of columns of sampleInterest
.
sampleInterest
A matrix of read counts obtained by an
affinity enrichment sequencing experiment for the samples of
interest. The number of rows must be equal to
length(windows)
. Each column contains the counts of
one sample.
cpgDens
A numeric vector containing the CpG density
for windows
. The length must be equal to
length(windows)
fOffset
A matrix where each column contains the normalizing offsets for one sample. The number of rows must be either equal to one or the number of windows.
priorTab
A list containing for each sample of interest
the prior parameters as determined by empBayes
.
methEst
A list containing the methylation estimates
as determined by methylEst
.
maskEmpBayes
A logical vector indicating which bins should be masked out in the empirical Bayes analysis. TRUE indicates to neglect the bin in the empirical Bayes approach.
signature(x = "BayMethList")
: Creates a BayMethList
object, keeping only the i
entries.
signature(x= "BayMethList")
: gets the number of
genomic regions included.
signature(x = "BayMethList")
: replace the
control
slot
signature(object = "BayMethList")
: extract the
control
matrix slot.
signature(x = "BayMethList")
: replace the
cpgDens
slot
signature(object = "BayMethList")
: extract the
cpgDens
slot.
signature(x = "BayMethList")
:
replace the sampleInterest
slot
signature(object = "BayMethList")
:
extract the sampleInterest
matrix slot.
signature(object = "BayMethList")
:
show an overview of the object
signature(x = "BayMethList")
:
replace the windows
slot
signature(object = "BayMethList")
:
extract the windows
GRanges slot.
signature(x = "BayMethList")
:
replace the fOffset
slot
signature(object = "BayMethList")
:
extract the fOffset
slot.
signature(x = "BayMethList")
:
replace the priorTab
slot
signature(object = "BayMethList")
:
extract the priorTab
slot.
signature(x = "BayMethList")
:
replace the methEst
slot
signature(object = "BayMethList")
:
extract the methEst
slot.
signature(x = "BayMethList")
:
replace the maskEmpBayes
slot
signature(object = "BayMethList")
:
extract the maskEmpBayes
slot.
signature(object = "BayMethList")
:
get the number of provided SssI samples.
signature(object = "BayMethList")
:
get the number of provided samples of Interest.
Andrea Riebler and Mark Robinson
determineOffset, empBayes, methylEst
if(require(BSgenome.Hsapiens.UCSC.hg18)){
windows <- genomeBlocks(Hsapiens, chrs="chr21", width=100, spacing=100)
cpgdens <- cpgDensityCalc(windows, organism=Hsapiens,
w.function="linear", window=700)
co <- matrix(rnbinom(length(windows), mu=10, size=2), ncol=1)
sI <- matrix(rnbinom(2*length(windows), mu=5, size=2), ncol=2)
bm <- BayMethList(windows=windows, control=co, sampleInterest=sI,
cpgDens=cpgdens)
cat("Number of genomic regions", length(bm), "\n")
cat("Number of fully methylated control samples:", ncontrol(bm), "\n")
cat("Number of samples of interest:", nsampleInterest(bm), "\n")
bm[2:20]
}
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.