Question: exomeCopy error with compileCopyCountSegments
gravatar for ramakrishnas
4 months ago by
ramakrishnas0 wrote:

(updated error message)

I am getting an error message with the exomecopy, compileCopyCountSegments


Error in FUN(X[[i]], ...) :

  trying to get slot "path" from an object of a basic class ("NULL") with no slots

Calls: compileCopyCountSegments -> lapply -> lapply -> FUN -> lapply -> lapply -> FUN

Execution halted

I have tried the package before with other datasets but never saw this error (see below), one thing that I changed is the reference genome. previously, I used genome build with "chr" prefix and now without. don't know if that could cause an issue. I was wondering if you would have any thoughts what I might be doing wrong to get this error. I will be happy to share the rdata object if you would need to look at it. 

thanks for you kind help




ADD COMMENTlink modified 4 months ago • written 4 months ago by ramakrishnas0
gravatar for Michael Love
4 months ago by
Michael Love17k
United States
Michael Love17k wrote:

I’d guess it has to do with updated versions of software, which changed the structure of the fit list object. Is it possible that versions changed before the last step and does it go away if you rerun exomeCopy function with the new version?

ADD COMMENTlink written 4 months ago by Michael Love17k

Thanks Michael for the replay.

keeping the installed version, I tested datasets generated with different genome builds. analysis with hg19 build with 'chr' works fine but grch37 build is giving this error. would you think the error is from a other dependent software that is used in fit.list object?



ADD REPLYlink written 4 months ago by ramakrishnas0

There's nothing particular to "chr" in the code that's giving you an error (copied below). compileCopyCountSegments() is pretty simply, and just a double loop over samples and over chromosomes.

Do you get an error with running copyCountSegments() alone on a single "fit" of class ExomeCopy?

copyCountSegments <- function(object) {
  x <- object@path
  changes <- which(x[-length(x)] != x[-1]) + 1
  if (length(changes) > 0) {
    range.start <- c(1,changes)
    range.end <- c(changes-1,length(x))
  } else {
    range.start <- 1
    range.end <- length(x)
  targeted.bp <- sapply(1:length(range.start),function(i) sum(width(object@ranges)[[1]][range.start[i]:range.end[i]]))
  log.odds <- sapply(1:length(range.start),function(i) sum(object@log.odds[range.start[i]:range.end[i]]))
  gr <- GRanges(seqnames(object@ranges)[1],
                nranges=(range.end - range.start + 1),
  genome(gr) <- genome(object@ranges)

compileCopyCountSegments <- function(fit.list) {
  sample.res <- lapply(fit.list,function(seq.list) {
    seq.res <- lapply(seq.list, copyCountSegments),unname(seq.res))
ADD REPLYlink written 4 months ago by Michael Love17k
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