binomialTestMethylation {methimpute} | R Documentation |
Call methylation status of cytosines (or bins) with a binomial test.
binomialTestMethylation(data, conversion.rate, min.coverage = 3, p.threshold = 0.05)
data |
A |
conversion.rate |
A conversion rate between 0 and 1. |
min.coverage |
Minimum coverage to consider for the binomial test. |
p.threshold |
Significance threshold between 0 and 1. |
The function uses a binomial test with the specified conversion.rate
. P-values are then multiple testing corrected with the Benjamini & Yekutieli procedure. Methylated positions are selected with the p.threshold
.
A vector with methylation statuses.
## Get some toy data file <- system.file("data","arabidopsis_toydata.RData", package="methimpute") data <- get(load(file)) data$binomial <- binomialTestMethylation(data, conversion.rate=0.998)