GOSemSim - slow for BP terms
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nooshin ▴ 290
@nooshin-5239
Last seen 2.8 years ago

Hi,

I'm using GOSemSim to find similarity between genes based on their annotation with respect to BP, CC, and MF.

I realized that the speed of the algorithm for BP terms are very much slow.

If I ran my algorithm even in parallel with these 3 terms, CC and MF is going to finish, and the BP starts to run.

I'm running my analysis on the cluster and I have enough node and memory available. So, these are no points to stop my calculation.

Thank you in advance for your help!

Best,

NU

and here is my sessionInfo:

 

> sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS

Matrix products: default
BLAS: /apps/devel/R/3.4.3/lib64/R/lib/libRblas.so
LAPACK: /apps/devel/R/3.4.3/lib64/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8
 [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8
 [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C
[10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
[1] org.At.tair.db_3.5.0 AnnotationDbi_1.40.0 IRanges_2.12.0
[4] S4Vectors_0.16.0     Biobase_2.38.0       BiocGenerics_0.24.0
[7] GOSemSim_2.4.1

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.17    GO.db_3.5.0     digest_0.6.15   DBI_1.0.0
 [5] RSQLite_2.1.1   blob_1.1.1      tools_3.4.3     bit64_0.9-7
 [9] bit_1.1-14      compiler_3.4.3  pkgconfig_2.0.1 memoise_1.1.0

 

gosemsim go enrichment go semantic similarity • 467 views
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