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Question: goseq - supportedOrganisms error
0
gravatar for starbug16
16 months ago by
starbug160
starbug160 wrote:

Hi,

I've been following the vignette, but I keep getting the following error with supportedOrganisms() from goseq:

Error in matrix(unlist(pairs), nrow = 2) :
  'data' must be of a vector type, was 'NULL'

Is there something I am doing wrong?

Many thanks in advance!!

Victoria


R version 3.3.2 (2016-10-31) -- "Sincere Pumpkin Patch"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin13.4.0 (64-bit)

> library(goseq)
Loading required package: BiasedUrn
Loading required package: geneLenDataBase

> supportedOrganisms()
Loading required package: rtracklayer
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB,
    parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following objects are masked from ‘package:base’:

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Error in matrix(unlist(pairs), nrow = 2) :
  'data' must be of a vector type, was 'NULL'
> traceback()
14: matrix(unlist(pairs), nrow = 2)
13: .local(object, ...)
12: ucscCart(x)
11: ucscCart(x)
10: genome(ucscCart(x))
9: genome(x)
8: genome(x)
7: `genome<-`(`*tmp*`, value = "hg19")
6: `genome<-`(`*tmp*`, value = "hg19")
5: GenomicFeatures:::supportedUCSCtables()
4: is.factor(var)
3: unfactor(GenomicFeatures:::supportedUCSCtables())
2: supportedGeneIDs()
1: supportedOrganisms()

ADD COMMENTlink modified 16 months ago by Gordon Smyth34k • written 16 months ago by starbug160

Hi Victoria,

Thanks for reporting this. The parsing in the underlying function 

rtracklayer:::.getOrganism()

is broken because the web page it queried has been overhauled. It may take a little while to fix this. We'll report back when it's done.

Valerie

ADD REPLYlink written 16 months ago by Valerie Obenchain ♦♦ 6.5k

Oops, not related. Sorry for the misdiagnosis.

Valerie

ADD REPLYlink written 16 months ago by Valerie Obenchain ♦♦ 6.5k
0
gravatar for James W. MacDonald
16 months ago by
United States
James W. MacDonald46k wrote:

This has actually already been fixed, as part of A: Error in Gviz | IdeogramTrack

> z <- supportedOrganisms()
head(z)
>
    Genome         Id  Id Description Lengths in geneLeneDataBase
12 anoCar1    ensGene Ensembl gene ID                        TRUE
13 anoGam1    ensGene Ensembl gene ID                        TRUE
14 apiMel2    ensGene Ensembl gene ID                        TRUE
56 bosTau2 geneSymbol     Gene Symbol                        TRUE
15 bosTau3    ensGene Ensembl gene ID                        TRUE
57 bosTau3 geneSymbol     Gene Symbol                        TRUE
   GO Annotation Available
12                   FALSE
13                    TRUE
14                   FALSE
56                    TRUE
15                    TRUE
57                    TRUE
ADD COMMENTlink written 16 months ago by James W. MacDonald46k

But that doesn't mean that rtracklayer:::.getOrganism is OK - that is still busted, because of changes at UCSC.

ADD REPLYlink written 16 months ago by James W. MacDonald46k
0
gravatar for Gordon Smyth
16 months ago by
Gordon Smyth34k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth34k wrote:

It's worth pointing out something is often overlooked:

In most cases, your gene quantification program (featureCounts, htseq-count etc) will return information about gene length, and you can pass this information directly to goseq. So, in most cases, you can use goseq without needing to access the gene length database or to deal with all the infrastructure associated with supported organisms.

ADD COMMENTlink modified 16 months ago • written 16 months ago by Gordon Smyth34k
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