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!
and here is my 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
 LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
 LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
 LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
 LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
attached base packages:
 stats4 parallel stats graphics grDevices utils datasets
 methods base
other attached packages:
 org.At.tair.db_3.5.0 AnnotationDbi_1.40.0 IRanges_2.12.0
 S4Vectors_0.16.0 Biobase_2.38.0 BiocGenerics_0.24.0
loaded via a namespace (and not attached):
 Rcpp_0.12.17 GO.db_3.5.0 digest_0.6.15 DBI_1.0.0
 RSQLite_2.1.1 blob_1.1.1 tools_3.4.3 bit64_0.9-7
 bit_1.1-14 compiler_3.4.3 pkgconfig_2.0.1 memoise_1.1.0