poissonGoodnessOfFit(BSseq, nQuantiles = 10^5)
binomialGoodnessOfFit(BSseq, method = c("MLE"), nQuantiles = 10^5)
"print"(x, ...)
"plot"(x, type = c("chisq", "pvalue"), plotCol = TRUE, qqline = TRUE, pch = 16, cex = 0.75, ...)
BSseq
.poissonGoodnessOfFit
or binomialGoodnessOfFit
).qqline
.qqplot
(for
plot
) or ignored (for print
).poissonGoodnessOfFit
and binomialGoodnessOfFit
returns
an object of class chisqGoodnessOfFit
which is a list with components
BSseq
objects. For each methylation loci, the Poisson
goodness of fit statistic tests whether the coverage (at that loci) is
independent and identically Poisson distributed across the samples.
In a similar fashion, the Binomial goodness of fit statistic tests
whether the number of reads supporting methylation are independent and
identically binomial distributed across samples (with different size
parameters given by the coverage vector). These functions do not handle NA
values.
qqplot
.
if(require(bsseqData)) {
data(BS.cancer.ex)
BS.cancer.ex <- updateObject(BS.cancer.ex)
gof <- poissonGoodnessOfFit(BS.cancer.ex)
plot(gof)
}
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