Question: igraph PoTRA error
0
gravatar for plink_9857
19 months ago by
plink_985750
United States
plink_985750 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 • 582 views
ADD COMMENTlink modified 19 months ago by genomax73k • written 19 months ago by plink_985750

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 19 months ago by Jean-Karim Heriche21k
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