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Added na.rm parameter for getMeth regions. #45

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Added na.rm parameter for getMeth regions. #45

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fe4f755
added remove NA to getMeth to allow returning NA for regions if any C…
Oct 24, 2016
0e4c82a
Added manual for na.rm parameter in getMeth
Oct 24, 2016
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7 changes: 4 additions & 3 deletions R/BSseq_utils.R
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Original file line number Diff line number Diff line change
Expand Up @@ -35,7 +35,8 @@ orderBSseq <- function(BSseq, seqOrder = NULL) {


getMeth <- function(BSseq, regions = NULL, type = c("smooth", "raw"),
what = c("perBase", "perRegion"), confint = FALSE, alpha = 0.95) {
what = c("perBase", "perRegion"), confint = FALSE, alpha = 0.95,
na.rm = TRUE) {
p.conf <- function(p, n, alpha) {
z <- abs(qnorm((1 - alpha)/2, mean = 0, sd = 1))
upper <- (p + z^2/(2*n) + z*sqrt( (p*(1-p) + z^2/(4*n)) / n)) /
Expand Down Expand Up @@ -96,12 +97,12 @@ getMeth <- function(BSseq, regions = NULL, type = c("smooth", "raw"),
if(what == "perRegion") {
if(type == "smooth") {
out <- lapply(mmsplit, function(xx) {
colMeans(getBSseq(BSseq, "trans")(getBSseq(BSseq, "coef")[xx,,drop = FALSE]), na.rm = TRUE)
colMeans(getBSseq(BSseq, "trans")(getBSseq(BSseq, "coef")[xx,,drop = FALSE]), na.rm = na.rm)
})
}
if(type == "raw") {
out <- lapply(mmsplit, function(xx) {
colMeans(getBSseq(BSseq, "M")[xx,,drop = FALSE] / getBSseq(BSseq, "Cov")[xx,,drop = FALSE], na.rm = TRUE)
colMeans(getBSseq(BSseq, "M")[xx,,drop = FALSE] / getBSseq(BSseq, "Cov")[xx,,drop = FALSE], na.rm = na.rm)
})
}
out <- do.call(rbind, out)
Expand Down
9 changes: 7 additions & 2 deletions man/getMeth.Rd
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Expand Up @@ -8,7 +8,8 @@
}
\usage{
getMeth(BSseq, regions = NULL, type = c("smooth", "raw"),
what = c("perBase", "perRegion"), confint = FALSE, alpha = 0.95)
what = c("perBase", "perRegion"), confint = FALSE, alpha = 0.95,
na.rm = TRUE)
}
\arguments{
\item{BSseq}{An object of class \code{BSseq}.}
Expand All @@ -20,6 +21,7 @@ getMeth(BSseq, regions = NULL, type = c("smooth", "raw"),
methylation estimates (see below). This is only supported if
\code{what} is equal to \code{perBase}.}
\item{alpha}{alpha value for the confidence interval.}
\item{na.rm}{whether to ignore NA methylation values for region averages}
}
\note{
A \code{BSseq} object needs to be smoothed by the function
Expand All @@ -44,7 +46,10 @@ getMeth(BSseq, regions = NULL, type = c("smooth", "raw"),
corresponding to a genomic region (and each row of the matrix being a
loci inside the region). If \code{what = "perRegion"} the function
returns a matrix, with each row corresponding to a region and
containing the average methylation level in that region.
containing the average methylation level in that region. If
\code{na.rm = FALSE}, the average methylation level of regions is given
as NA if any CpG in the region has a coverage of 0 and therefore
methylation level of NA.
}
\references{
A Agresti and B Coull.
Expand Down