## ---- include = FALSE---------------------------------------------------------
library(knitr)
knitr::opts_chunk$set(
    collapse = TRUE,
    comment = "#>"
)

## ----setup--------------------------------------------------------------------
suppressMessages(library(synaptome.db))
suppressMessages(library(dplyr))
library(pander)

## ----gene_info----------------------------------------------------------------
t <- getGeneInfoByEntrez(1742) 
head(t)

t <- getGeneInfoByName("CASK")
head(t)

t <- getGeneInfoByName(c("CASK", "DLG2"))
head(t)                      

## ----findIDs------------------------------------------------------------------
t <- findGenesByEntrez(c(1742, 1741, 1739, 1740))
head(t)

t <- findGenesByName(c("SRC", "SRCIN1", "FYN"))
head(t)


## ----disease------------------------------------------------------------------
t <- getGeneDiseaseByName (c("CASK", "DLG2", "DLG1"))
head(t)

t <- getGeneDiseaseByEntres (c(8573, 1742, 1739))
head(t)


## ----PPI----------------------------------------------------------------------
t <- getPPIbyName(
    c("CASK", "DLG4", "GRIN2A", "GRIN2B","GRIN1"), 
    type = "limited")
head(t)

t <- getPPIbyEntrez(c(1739, 1740, 1742, 1741), type='induced')
head(t)


## ----compPPI------------------------------------------------------------------
#getting the list of compartment
comp <- getCompartments()
pander(comp)

#getting all genes for postsynaptic compartment
gns <- getAllGenes4Compartment(compartmentID = 1) 
head(gns)

#getting full PPI network for postsynaptic compartment
ppi <- getPPIbyIDs4Compartment(gns$GeneID,compartmentID =1, type = "induced")
head(ppi)


## ----regPPI-------------------------------------------------------------------
#getting the full list of brain regions
reg <- getBrainRegions()
pander(reg)

#getting all genes for mouse Striatum
gns <- getAllGenes4BrainRegion(brainRegion = "Striatum",taxID = 10090)
head(gns)

#getting full PPI network for postsynaptic compartment
ppi <- getPPIbyIDs4BrainRegion(
    gns$GeneID, brainRegion = "Striatum", 
    taxID = 10090, type = "limited")
head(ppi)

## ----PPI_igraph,fig.width=7,fig.height=7,out.width="70%",fig.align = "center"----
library(igraph)
g<-getIGraphFromPPI(
    getPPIbyIDs(c(48, 129,  975,  4422, 5715, 5835), type='lim'))
plot(g,vertex.label=V(g)$RatName,vertex.size=25)

## ----PPI_table----------------------------------------------------------------
tbl<-getTableFromPPI(getPPIbyIDs(c(48, 585, 710), type='limited'))
tbl

## ----sessionInfo, echo=FALSE, results='asis', class='text', warning=FALSE-----
c<-devtools::session_info()
pander::pander(t(data.frame(c(c$platform))))
pander::pander(as.data.frame(c$packages)[,-c(4,5,10,11)])