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Disease_genomics_Periodontitis.R
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Disease_genomics_Periodontitis.R
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# Installation instructions
#library(devtools)
#install_bitbucket("ibi_group/disgenet2r", force=TRUE)
library(disgenet2r)
disgenet_api_key <- get_disgenet_api_key(
email = "[email protected]",
password = "********" )
Sys.setenv(DISGENET_API_KEY= disgenet_api_key)
setwd("/Users/enrique/Dropbox/Periodontitis_Genomics")
POD <- disease2gene(disease = "C0031099",
database = "ALL",
score = c(0.3,1)
)
POD
plot(POD,
class = "Network",
prop = 10)
plot(POD,
class="ProteinClass")
#??"DataGeNET.DGN"
# PDA <-extract(POD)
#
# PDA
PDD <-POD@qresult
## PDD <- POD@qresult ## alternative to extract for a DataGeNET.DGN object
PDD
## Diseases_sharing_genes_with Periodontitis
PGSD <- c("C0031099","C0948089","C0023465","C0023479",
"C0001418","C0001973","C0002395","C0002726",
"C0002871","C0038013","C0003467","C0004096",
"C0004153","C0004238","C0006840","C4048328",
"C0024117","C1561643","C1956346","C0010068",
"C0010346","C0011581","C0242339","C0376618",
"C0014859","C0031069","C0017661","C0018213",
"C0018520","C0278996","C0018965","C0019080",
"C0019158","C1857728","C0019348","C0019829",
"C0020429","C0020456","C0085580","C0021390",
"C0021655","C0684249","C0024796","C0023418",
"C0026640","C0026764","C0027051","C0400966",
"C0028754","C0585362","C0029456","C0235974",
"C0030297","C0030567","C1704436","C0001623",
"C0032285","C0032460","C0033687","C0033860",
"C0003873","C0036690","C1527336","C0520679",
"C0038454","C0024141","C0040034","C0011854",
"C0009324","C0346153","C0006142","C0678222",
"C0011860","C1852092","C0011849","C0019693",
"C0376358","C2931456","C4722327","C0015499")
PODNet <- disease2gene(
disease = PGSD,
database = "CURATED",
score =c(0.4,1),
verbose = TRUE )
plot(PODNet,
class = "Network",
prop = 2)
plot(PODNet,
class="Heatmap",
limit =30,
cutoff=0.2)
plot(PODNet,
class="ProteinClass")
# PODNet
POT <-extract(PODNet)
#POT
write.csv(POT, file="Diseases_Genes_Periodontitis_extract.csv")
PDRS<-PODNet@qresult
#PDRS
write.csv(PDRS, file="Diseases_Genes_Periodontitis.csv")
#### Diseasome networks
DisPer <- disease2disease_by_gene(
disease = "C0031099",
database = "CURATED", ndiseases = 100 )
DPeri <- extract(DisPer)
plot(DisPer,
class = "Network",
layout="layout.lgl" ,
prop = 0.2 )
plot( DisPer,
class = "Diseasome",
layout="layout.lgl" ,
prop = 0.1 )
plot( DisPer,
class="Barplot")
write.csv(DPeri, file="Top_Diseases_shared_genes_Periodontitis.csv")
PerDis <-DPeri[c("disease1_name", "disease2_name","jaccard_genes","ngenes", "pvalue")]
write.csv(PerDis, file="Top_Diseases_shared_genes_Periodontitis_abridged.csv")