Using mgeneSim with Ensembl ids
1
0
Entering edit mode
@saadmurtazakhan-6782
Last seen 7 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 • 841 views
ADD COMMENT
0
Entering edit mode
Guangchuang Yu ★ 1.2k
@guangchuang-yu-5419
Last seen 7 months 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
0
Entering edit mode

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
0
Entering edit mode

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
0
Entering edit mode

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
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 188 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6