On Thu, Apr 23, 2009 at 3:22 PM, <[email protected]> wrote:
>
> Hi Deepayan,
>
> When I do
>
> control1 <- combineLaneReads(c(expt1_analysis1[c("1", "2")],
> expt1_analysis2[c("3", "4")]))
>
> is there a way to filter reads so that I only get one read per genomic
> position?
combineLaneReads is a very simple function:
combineLaneReads <- function(laneList, chromList = names(laneList[[1]])) {
names(chromList) = chromList ##to get the return value named
GenomeData(lapply(chromList,
function(chr) {
list("+" = unlist(lapply(laneList,
function(x) x[[chr]][["+"]]), use.names = FALSE),
"-" = unlist(lapply(laneList,
function(x) x[[chr]][["-"]]), use.names = FALSE))
}))
}
and you can just wrap a unique() around the unlist() to make the start
positions unique. But why would you want that? Within a lane,
duplicates are likely to be PCR artifacts, but for data from different
lanes, aren't duplicates more likely to be real? We could easily add
an argument to support this if you have a valid use-case.
-Deepayan
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