Question: igraph PoTRA error
0
gravatar for plink_9857
13 months ago by
plink_985740
United States
plink_985740 wrote:

I need help troubleshooting the PoTRA program (which depends on igraph). The PoTRA's program functions, workspace file, etc can be found here: See the error message below.

https://github.com/GenomicsPrograms/PoTRA/tree/master/PoTRA%20Code

After running the following code:

First paste the functions in PoTRA_R.txt into R, load the PoTRA-example-data.rdata then,

library(BiocGenerics) <br>
library(graph) <br>
library(graphite) <br>
library(igraph) <br>
library(stats) <br>

humanKEGG <- pathways("hsapiens", "kegg") 


results.comb <-PoTRA.comb(mydata=mydata,genelist=genelist,Num.sample.normal=8,Num.sample.case=8,Pathway.database=humanKEGG[1:10],PR.quantile=0.95)

I received the following error message:

**Error in PoTRA.comb(mydata = mydata, genelist = genelist, Num.sample.normal = 8,  :
  object 'E.union.normal' not found**

Here is my sessionInfo()

> sessionInfo() <br>
R Under development (unstable) (2018-03-10 r74380) <br>
Platform: x86_64-w64-mingw32/x64 (64-bit) <br>
Running under: Windows 10 x64 (build 16299) <br>

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] org.Hs.eg.db_3.5.0   AnnotationDbi_1.41.4 IRanges_2.13.28      S4Vectors_0.17.35    Biobase_2.39.2       igraph_1.2.1         graphite_1.25.1     
[8] graph_1.57.1         BiocGenerics_0.25.3

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.16    magrittr_1.5    rappdirs_0.3.1  bit_1.1-12      R6_2.2.2        rlang_0.2.0     blob_1.1.0      httr_1.3.1      checkmate_1.8.5
[10] DBI_0.8         bit64_0.9-7     digest_0.6.15   tibble_1.4.2    memoise_1.1.0   RSQLite_2.0     compiler_3.5.0  pillar_1.2.1    backports_1.1.2
[19] pkgconfig_2.0.1
potra igraph • 456 views
ADD COMMENTlink modified 13 months ago by genomax65k • written 13 months ago by plink_985740

It looks like a bug in the PoTRA code. A quick look seems to point to an assignment to an element of the vector E.union.normal without having preallocated it first. This should be reported to the developers.

ADD REPLYlink written 13 months ago by Jean-Karim Heriche18k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 645 users visited in the last hour