Dear R-Users,
I am trying to perform network analysis using BioNet. I am having
issues with the runFastHeinz function. I extracted the sub network and
computed the scores and fed to the function. I even tried to run the
function from the example data in the help function. I get the same
error. Please help me solve this issue. I tried accessing the
igraph.from.graphNEL function from igraph as
igraph::igraph.from.graphNEL. But still it didnt fix the error.
library(DLBCL)
data(dataLym)
data(interactome)
interactome <- subNetwork(dataLym$label, interactome)
p.values <- dataLym$t.pval
names(p.values) <- dataLym$label
bum <- fitBumModel(p.values, plot=TRUE)
scores <- scoreNodes(network=interactome, fb=bum, fdr=0.0001)
module <- runFastHeinz(network=interactome, scores=scores)
Error in graph[[9]][[3]] : subscript out of bounds
> sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_SG LC_NUMERIC=C LC_TIME=en_SG
[4] LC_COLLATE=en_SG LC_MONETARY=en_SG LC_MESSAGES=en_SG
[7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_SG LC_IDENTIFICATION=C
attached base packages:
[1] grid stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] hash_2.2.6 DLBCL_1.3.5 BioNet_1.18.0
[4] RBGL_1.34.0 Biobase_2.18.0 BiocGenerics_0.4.0
[7] igraph0_0.5.5-3 maanova_1.28.0 samr_2.0
[10] matrixStats_0.8.12 impute_1.32.0 limma_3.14.4
[13] Rgraphviz_2.2.1 graph_1.36.2 GeneNet_1.2.8
[16] igraph_0.6.6 fdrtool_1.2.11 longitudinal_1.1.8
[19] corpcor_1.6.6 BiocInstaller_1.8.3
loaded via a namespace (and not attached):
[1] AnnotationDbi_1.20.7 DBI_0.2-7 IRanges_1.16.6
[4] parallel_2.15.1 R.methodsS3_1.5.2 RSQLite_0.11.4
[7] stats4_2.15.1 tools_2.15.1
Thanks,
Regards,
Kishor