igraph PoTRA error
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Entering edit mode
3.6 years ago
plink_9857 ▴ 50

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
igraph PoTRA • 990 views
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Entering edit mode

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.

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