Question: problem of GOSemSim R package operation
0
gravatar for zjzace
4.1 years ago by
zjzace0
China
zjzace0 wrote:

I have just installed GOSeSim package in Biocoundoctor. I tried to run genesim function. for the 1st time it worked. But after that, its giving below error :

Error in sqliteSendQuery(con, statement, bind.data) :
  expired SQLiteConnection

code:

library(parallel)
library(IRanges)
library(S4Vectors)
library(BiocGenerics)
library(Rcpp)
library(DBI)
library(AnnotationDbi)
library(Biobase)
library(GOSemSim)
library(org.Hs.eg.db)
data1 = read.table("/pub2/zjzace/genesim/coex1.txt", head=F, sep="\t")
data1 = as.factor(data1[,1])
n= length(data1)
for (i in 1:(n-1)){
g1=data1[i]
for (j in i:n){
g2=data1[j]
zz=geneSim(g1, g2, ont="MF", organism="human", measure="Wang", combine="avg")
similarity= paste(data1[i], data1[j], zz[[1]], sep="\t")
write.table(similarity, "/pub2/nsw/zjz/genesim/similarity-gene1-1.txt", append=T, col.names=F, row.names=F, sep="\t", quote=F)
}}

the data1 is only a colums gene id.

>sessionInfo()

R version 3.2.0 (2015-04-16)
Platform: x86_64-unknown-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server release 6.4 (Santiago)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] org.Hs.eg.db_3.2.3   GOSemSim_1.28.1      RSQLite_1.0.0       
 [4] AnnotationDbi_1.32.0 Biobase_2.30.0       DBI_0.3.1           
 [7] Rcpp_0.12.1          IRanges_2.4.1        S4Vectors_0.8.1     
[10] BiocGenerics_0.16.1 

loaded via a namespace (and not attached):
[1] GO.db_3.2.2

 

 

r package problem • 544 views
ADD COMMENTlink written 4.1 years ago by zjzace0
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