Sorry, I forgot to include the traceback in the last message. Here it
is.
10: stop(simpleError(msg, call = expr))
9: e$fun(obj, substitute(ex), parent.frame(), e$data)
8: list(args = IndexesChunks(.doRNG.stream = c(407L, -129130598L,
1725800531L, 1089509752L, -772932327L, 780595718L, 241179855L
)), argnames = c("idx", ".doRNG.stream"), evalenv = <environment>,
specified = character(0), combineInfo = list(fun = function (a,
...)
c(a, list(...)), in.order = TRUE, has.init = TRUE, init =
list(),
final = NULL, multi.combine = TRUE, max.combine = 100),
errorHandling = "stop", packages = c("bumphunter", "doRNG"
), export = NULL, noexport = NULL, options = list(), verbose =
FALSE) %dopar%
{
{
rngtools::RNGseed(.doRNG.stream)
}
{
idx <- get(foreach_argname)
smoothFunction(y = y[idx, ], x = x[idx], cluster =
cluster[idx],
weights = weights[idx, ], verbose = verbose,
...)
}
}
7: do.call("%dopar%", list(obj, ex), envir = parent.frame())
6: foreach_object %dorng% {
idx <- get(foreach_argname)
smoothFunction(y = y[idx, ], x = x[idx], cluster =
cluster[idx],
weights = weights[idx, ], verbose = verbose, ...)
}
5: smoother(y = permRawBeta, x = pos, cluster = cluster, weights =
weights,
smoothFunction = smoothFunction, verbose = subverbose)
4: bumphunterEngine(object, design = design, chr = chr, pos, cluster =
cluster,
coef = coef, cutoff = cutoff, cutoffQ = cutoffQ, maxGap =
maxGap,
smooth = smooth, smoothFunction = smoothFunction, useWeights =
useWeights,
B = B, verbose = verbose, ...)
3: .local(object, ...)
2: bumphunter(logtrans, matrix(c(rep(1,
ncol(final_Avg_beta_disc_NMF)),
as.numeric(factor(fullclinical[match(colnames(final_Avg_beta_disc_NMF)
,
fullclinical$OffTargetName), ]$NMF_2)) - 1), nrow =
ncol(final_Avg_beta_disc_NMF)),
chr_chr, chr_locs$MAPINFO, chr_clusters, smoothFunction =
loessByCluster,
smooth = TRUE)
1: bumphunter(logtrans, matrix(c(rep(1,
ncol(final_Avg_beta_disc_NMF)),
as.numeric(factor(fullclinical[match(colnames(final_Avg_beta_disc_NMF)
,
fullclinical$OffTargetName), ]$NMF_2)) - 1), nrow =
ncol(final_Avg_beta_disc_NMF)),
chr_chr, chr_locs$MAPINFO, chr_clusters, smoothFunction =
loessByCluster,
smooth = TRUE)
On Tue, Jun 3, 2014 at 1:37 PM, Jiayi Sun <monikasun88@gmail.com>
wrote:
> Hello,
>
> I have been trying to use bumphunter on my 450k data and I have been
> running into some problems with the smooth function using the option
of
> loessByCluster. I have tired both other smoothing functions
> runmedByCluster and locfitByCluster and these perform correctly
however I
> get this error when trying to use loessByCluster.
>
> Error in { :
> task 1 failed - "NA/NaN/Inf in foreign function call (arg 1)"
>
> I have called bumphunter with the following function:
>
> ### Run all chromosomes together
>
> chr_locs <- ordered by chromosome genomic location
> chr_chr <- chromosome information
> chr_clusters <- clusterMaker(chr_chr, chr_locs, maxGap = 400)
>
> logtrans <- log transformed beta-values
>
> chr_bumphunter <- bumphunter(logtrans,
> design matrix with first column of "1" and second column with
membership
> comparing 6 (0) samples to 89 samples (1),
> chr_chr, chr_locs, chr_clusters, smoothFunction = loessByCluster,
smooth
> = TRUE)
>
> This error always occurs when I am trying to do the permutations,
never on
> the normal data. This is the output from bumphunter.
>
> bumphunterEngine: Using a single core (backend: doSEQ, version:
1.4.2)
> bumphunterEngine: Computing coefficients.
> bumphunterEngine: Smoothing coefficients.
> bumphunterEngine cutoff: 1.123
> bumphunterEngine: Finding regions.
> bumphunterEngine: Performing 100 permutations.
> bumphunterEngine: Computing marginal permutation p-values.
> bumphunterEngine: Smoothing permutation coefficients.
>
> After which I see the error above. I have tired checking the
> logtransformed beta-values to see if I have any NAs or 1 but there
aren't
> any. Any idea what this error is coming from? I do have some very,
very
> small numbers approaching zero but I have tired even to change these
to
> 0.001 and it does not fix the error. Furthermore, it's only in the
> permutation portion where this error occurs so I thought this might
not be
> the problem.
>
> Any ideas what's going on?
>
> Thanks!
>
>
>
--
Jiayi Monika Sun
Rice University, Bioengineering '10
Baylor College of Medicine Graduate School, SCBMB
jmsun@bcm.edu
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