Error creating pool for permutation test (PeakPermTest from ChipPeakAnno)

Question

[Gema Sanz]

Hi,

I want to run permutation test to see the significance of the overlap for my chip-seq datasets. I'm following this example to remove blackspots and create the pool:

    data(HOT.spots)
    data(wgEncodeTfbsV3)
    hotGR <- reduce(unlist(HOT.spots))
    removeOl <- function(.ele){
        ol <- findOverlaps(.ele, hotGR)
        if(length(ol)>0) .ele <- .ele[-unique(queryHits(ol))]
        .ele
    }
    TAF <- removeOl(data[["TAF"]])
    TEAD4 <- removeOl(data[["Tead4"]])
    YY1 <- removeOl(data[["YY1"]])
    # we subset the pool to save demo time
    set.seed(1)
wgEncodeTfbsV3.subset <- wgEncodeTfbsV3[sample.int(length(wgEncodeTfbsV3), 2000)]
    pool <- new("permPool", grs=GRangesList(wgEncodeTfbsV3.subset), N=length(YY1))
    pt1 <- peakPermTest(YY1, TEAD4, pool=pool, seed=1, force.parallel=FALSE)
    plot(pt1)

In my case, I don't want to do any subset of wgEncodeTfbsV3, but Im getting this error when I try to do it without the subsampling step (A and B are in gRanges format):

data(HOT.spots)
data(wgEncodeTfbsV3)
hotGR <- reduce(unlist(HOT.spots))
removeOl <- function(.ele){
  ol <- findOverlaps(.ele, hotGR)
  if(length(ol)>0) .ele <- .ele[-unique(queryHits(ol))]
  .ele
}
A <- removeOl(TFA)
B <- removeOl(TFB)

set.seed(1)

pool <- new("permPool", grs=GRangesList(wgEncodeTfbsV3), N=length(B))

Error in validObject(ans) : 
  invalid class "GRanges" object: slots in class definition but not in object: "elementType"
Error during wrapup: no slot of name "elementType" for this object of class "GRanges"

Any ideas of what could be happening?

Thank you very much in advance!

Gema

Answer 1

[hukai916]

Sorry for the late reply!

Have you tried the latest version (v3.31.1) of ChIPpeakAnno? The example code on the latest manual does not subset wgEncodeTfbsV3 and it works fine: vignettes

BTW, for Bioconductor package questions, pls go to Bioconductor Support Site, which is actively monitored by developers.