Question: scan() error when using biomaRt::getBM()
0
gravatar for enricoferrero
4.2 years ago by
enricoferrero570
Switzerland
enricoferrero570 wrote:

I'm getting this type of error with some biomaRt queries:

library(biomaRt)
mart <- useMart("ensembl", "hsapiens_gene_ensembl")
chr <- c(1:22, "X", "Y", "MT")

structures <- getBM(
                 attributes=c("ensembl_gene_id",
                              "interpro",
                              "low_complexity",
                              "transmembrane_domain",
                              "signal_domain",
                              "ncoils"),
                 filters="chromosome_name",
                 values=chr,
                 mart=mart)

Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,  :
  line 70966 did not have 6 elements

functions <- getBM(
                 attributes=c("ensembl_gene_id",
                              "go_id",
                              "reactome"),
                 filters="chromosome_name",
                 values=chr,
                 mart=mart)

Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,  :
  line 2021629 did not have 3 elements

Both examples should be reproducible.

Any idea what could cause this to fail?

Thank you,

 

> sessionInfo()
R version 3.2.0 (2015-04-16)
Platform: x86_64-unknown-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server release 6.6 (Santiago)

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C               LC_TIME=en_GB.UTF-8        LC_COLLATE=C
 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=C              LC_PAPER=en_GB.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] biomaRt_2.24.0       BiocInstaller_1.18.4 vimcom_1.2-6         colorout_1.0-2       setwidth_1.0-4

loaded via a namespace (and not attached):
 [1] IRanges_2.2.7        XML_3.98-1.3         bitops_1.0-6         GenomeInfoDb_1.4.1   DBI_0.3.1            stats4_3.2.0
 [7] RSQLite_1.0.0        S4Vectors_0.6.3      tools_3.2.0          Biobase_2.28.0       RCurl_1.95-4.7       parallel_3.2.0
[13] BiocGenerics_0.14.0  AnnotationDbi_1.30.1
biomart error scan • 883 views
ADD COMMENTlink modified 4.2 years ago • written 4.2 years ago by enricoferrero570
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