Question

Using mgeneSim with Ensembl ids

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saadmurtazakhan ▴ 10

@saadmurtazakhan-6782

Last seen 8 months ago

United States

Hi,

I have a list of Ensembl ids that I am trying to use with mgeneSim function. Everytime I run it it returns a 0X0 matrix with the following warning message :-

1: In is.na(go) : is.na() applied to non-(list or vector) of type 'NULL'

Here is the code that I use :-

mytestgenes <- c("ENSG00000271793","ENSG00000172789","ENSG00000264364","ENSG00000120533","ENSG00000174871","ENSG00000112531")

GOsim_matrix <- mgeneSim(genes=mytestgenes,ont="MF",organism="human",measure="Wang",verbose=T)

I am assuming that GOsemsim only works with enrez ids and I was wondering if there is a way to make it work with Ensembl ids.

regards

Ensembl GOsemsim GO semantic similarity • 1.8k views

ADD COMMENT • link updated 8.4 years ago by Guangchuang Yu ★ 1.2k • written 8.4 years ago by saadmurtazakhan ▴ 10

score 0 · Answer 1 · 2016-08-24

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Guangchuang Yu ★ 1.2k

@guangchuang-yu-5419

Last seen 8 weeks ago

China/Guangzhou/Southern Medical Univer…

this was supported in devel branch. see the vignette https://bioconductor.org/packages/devel/bioc/vignettes/GOSemSim/inst/doc/GOSemSim.html

ADD COMMENT • link 8.4 years ago Guangchuang Yu ★ 1.2k

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This is my session info.

R version 3.3.0 (2016-05-03)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS release 6.7 (Final)

locale:
[1] C

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

other attached packages:
[1] GOSemSim_1.30.3 BiocInstaller_1.22.3

loaded via a namespace (and not attached):
[1] org.Hs.eg.db_3.3.0 IRanges_2.6.1 parallel_3.3.0
[4] DBI_0.4-1 tools_3.3.0 Rcpp_0.12.6
[7] Biobase_2.32.0 AnnotationDbi_1.34.4 RSQLite_1.0.0
[10] S4Vectors_0.10.2 BiocGenerics_0.18.0 stats4_3.3.0
[13] GO.db_3.3.0

What version of R would you think would work with that given in the vignette.

PS: I dont have admin priveleges

ADD REPLY • link 8.4 years ago saadmurtazakhan ▴ 10

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if you have no idea how to install devel branch, I recommend you stick with release branch.

Instead you can convert ensemble id to entrez gene id (e.g. using bitr).

ADD REPLY • link 8.4 years ago Guangchuang Yu ★ 1.2k

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What should I change below to make bitr work.

bitr(mytestgenes, fromType="ENSEMBLID", toType="ENTREZID", OrgDb="org.Hs.eg.db")
Error in bitr(mytestgenes, fromType = "ENSEMBLID", toType = "ENTREZID",  : 
  unused argument (OrgDb = "org.Hs.eg.db")

ADD REPLY • link 8.3 years ago saadmurtazakhan ▴ 10

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pls make sure clusterProfiler was loaded correctly and you are using the latest release version.

ADD REPLY • link 8.3 years ago Guangchuang Yu ★ 1.2k