Running RnBeads (v1.2, BioC 3.2) fails at multiple steps with this error message: Error in DataFrame(..., check.names = FALSE) : formal argument "check.names" matched by multiple actual arguments This can be traced to
11: DataFrame(..., check.names = FALSE)
10: is(mcols, "DataFrame")
9: newGRanges("GRanges", seqnames = seqnames, ranges = ranges, strand = strand,
mcols = DataFrame(..., check.names = FALSE), seqlengths = seqlengths,
seqinfo = seqinfo)
8: (function (seqnames = Rle(), ranges = NULL, strand = NULL, ...,
seqlengths = NULL, seqinfo = NULL)
{
newGRanges("GRanges", seqnames = seqnames, ranges = ranges,
strand = strand, mcols = DataFrame(..., check.names = FALSE),
seqlengths = seqlengths, seqinfo = seqinfo)
})(seqnames = c("chr1", "chr1", "chr1", "chr1", "chr1", "chr1",
...
7: do.call(GRanges, param.list)
6: data.frame2GRanges(annot.s, chrom.column = "Chromosome", start.column = "Start",
end.column = "End", strand.column = "Strand", assembly = assembly(rnb.set),
sort.result = FALSE)
5: rnb.find.relative.site.coord(rnb.set, region.type, extend.by = extend.by)
4: rnb.plot.region.site.density(rnb.set, reg)
3: rnb.section.region.description(report, rnb.set, r.types)
2: rnb.run.exploratory(rnb.set, dir.reports)
1: rnb.run.analysis(dir.reports = report.dir, sample.sheet = sample.annotation,
data.dir = idat.dir, data.type = "infinium.idat.dir")
The reason seems to be a recent change in GRanges (I'm using v 1.22.0) that does no longer require/accept check.names=F for maintaining column names:
p = list() p[["seqnames"]]=c("2","3","4") p[["ranges"]]=IRanges(start=c(1,2,3), end=c(2,3,4), names=c("A","B","C")) p[["strand"]]=c("+","+","-") p[["var1"]]=c(7,8,9) p[["Variable 2"]] = c(100,101,102) do.call(GRanges, p)
GRanges object with 3 ranges and 2 metadata columns:
seqnames ranges strand | var1 Variable 2
<Rle> <IRanges> <Rle> | <numeric> <numeric>
A 2 [1, 2] + | 7 100
B 3 [2, 3] + | 8 101
C 4 [3, 4] - | 9 102
-------
seqinfo: 3 sequences from an unspecified genome; no seqlengths
p[["check.names"]]=FALSE do.call(GRanges, p)
Error in DataFrame(..., check.names = FALSE) :
formal argument "check.names" matched by multiple actual arguments
Removing the "check.names" parameter in function data.frame2GRanges should make the pipeline work again.
> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.3 LTS
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_GB.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
other attached packages:
[1] RnBeads_1.2.0
[2] plyr_1.8.3
[3] methylumi_2.16.0
[4] minfi_1.16.0
[5] bumphunter_1.10.0
[6] locfit_1.5-9.1
[7] iterators_1.0.8
[8] foreach_1.4.3
[9] Biostrings_2.38.0
[10] XVector_0.10.0
[11] SummarizedExperiment_1.0.0
[12] lattice_0.20-33
[13] FDb.InfiniumMethylation.hg19_2.2.0
[14] org.Hs.eg.db_3.2.3
[15] RSQLite_1.0.0
[16] DBI_0.3.1
[17] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
[18] GenomicFeatures_1.22.0
[19] AnnotationDbi_1.32.0
[20] reshape2_1.4.1
[21] scales_0.3.0
[22] Biobase_2.30.0
[23] illuminaio_0.12.0
[24] matrixStats_0.15.0
[25] limma_3.26.0
[26] gridExtra_2.0.0
[27] gplots_2.17.0
[28] ggplot2_1.0.1
[29] fields_8.3-5
[30] maps_3.0.0-2
[31] spam_1.2-1
[32] ff_2.2-13
[33] bit_1.1-12
[34] cluster_2.0.3
[35] RColorBrewer_1.1-2
[36] MASS_7.3-44
[37] GenomicRanges_1.22.0
[38] GenomeInfoDb_1.6.0
[39] IRanges_2.4.1
[40] S4Vectors_0.8.0
[41] BiocGenerics_0.16.0
Do you know how to remove the "check.names" parameter in function data.frame2GRanges? Thanks.
Did anyone find a solution to this issue? I'm having the same problem
Hi,
I see this commit in the devel branch of RnBeads:
but nothing in the release branch. Would be good if the authors/maintainers of RnBeads could also fix the release branch. Also would be nice to hear from them here.
Cheers,
H.
@Herve Pages, how do I view your commit to the devel branch of RnBeads? I'm not sure which path to specify when I go to checkout the changes in the log above. For example, how would I view your changes, using a Terminal command svn checkout XXX?
The commit is from Yassen (
y.assenov
), not mine. See it with:It looks like this change and others have been backported to the release version of RnBeads:
Cheers,
H.