inst/doc/case_study.R

In psygenet2r: psygenet2r - An R package for querying PsyGeNET and to perform comorbidity studies in psychiatric disorders

## ----pubmed1, fig.cap="Psychiatric disorders in PubMed. It has been obtained querying **psychiatric disorder [Title/Abstract] from 1955 to 2016**.", echo=FALSE, fig.wide = TRUE----
library(ggplot2)

data.file <- system.file(
  paste0("extdata", .Platform$file.sep, "psychiatricDisordersPubmed.csv"), 
  package="psygenet2r"
)

pmid <- read.delim(data.file, header=TRUE, sep=",")
pmid <- pmid[pmid$year<2017 & pmid$year>1950,]

pmid$year <- factor(pmid$year)
labels <- as.integer(seq(1950, 2016, by=5))

p <- ggplot(pmid, aes ( x = year, y = count ) ) +
    geom_bar ( stat = "identity", fill = "grey" ) +
    labs ( title = "Number of publications for psychiatric disorders in PubMed" , x = "year", y = "# of pmids") +
    theme_classic( ) + 
    scale_x_discrete(breaks=labels, labels=as.character(labels))+
    theme( plot.margin = grid::unit ( x = c ( 5, 15, 5, 15 ), units = "mm" ),
                                     axis.line = element_line ( size = 0.7, color = "black" ), 
           text = element_text ( size = 14 ) ,
           axis.text.x = element_text ( angle = 45, size = 11, hjust = 1 ) )

p

## ----bioC, eval=FALSE---------------------------------------------------------
#  if (!requireNamespace("BiocManager", quietly=TRUE))
#      install.packages("BiocManager")
#  BiocManager::install( "psyGeNET2R" )

## ----load_library, messages=FALSE---------------------------------------------
library( psygenet2r )

## ----genes--------------------------------------------------------------------
genesOfInterest <- c("ADCY2", "AKAP13", "ANK3", "ANKS1A", 
"ATP6V1G3", "ATXN1", "C11orf80", "C15orf53", "CACNA1C", 
"CACNA1D", "CACNB3", "CROT", "DLG2", "DNAJB4", "DUSP22", 
"FAM155A", "FLJ16124", "FSTL5", "GATA5", "GNA14", "GPR81", 
"HHAT", "IFI44", "ITIH3", "KDM5B", "KIF1A", "LOC150197", 
"MAD1L1", "MAPK10", "MCM9", "MSI2", "NFIX", "NGF", "NPAS3", 
"ODZ4", "PAPOLG", "PAX1", "PBRM1", "PTPRE", "PTPRT", 
"RASIP1", "RIMBP2", "RXRG", "SGCG", "SH3PXD2A", "SIPA1L2",
"SNX8", "SPERT", "STK39", "SYNE1", "THSD7A", "TNR", 
"TRANK1", "TRIM9", "UBE2E3", "UBR1", "ZMIZ1", "ZNF274")

## ----search_multiple----------------------------------------------------------
m1 <- psygenetGene(
    gene     = genesOfInterest, 
    database = "ALL",
    verbose  = FALSE,
    warnings = FALSE
)
m1

## ----gene-disease, fig.height=8, fig.width=8, fig.cap = "Gene-Disease Association Network", fig.wide = TRUE----
plot( m1 )

## ----gene-psy, fig.cap="Association type barplot according to psychiatric category", fig.wide = TRUE----
geneAttrPlot( m1, type = "evidence index" )

## ----panther, fig.cap="Panther class analysis of the genes of interest.", message=FALSE, warning=FALSE, fig.wide = TRUE----
pantherGraphic( genesOfInterest, "ALL")

## ----gene-disease-2, fig.cap="Gene-Disease Association Heatmap", fig.wide = TRUE----
plot( m1, type="GDA heatmap")

## ----pubmed2, fig.cap="Publications that report each gene association with bipolar disorder", fig.wide = TRUE----
plot( m1, name="bipolar disorder", type="publications")

## ----sentences1_query---------------------------------------------------------
m2 <- psygenetGeneSentences(
    geneList = genesOfInterest, 
    database = "ALL"
)
m2

## ----sentences2_extraction, warnings=FALSE------------------------------------
sentences <- extractSentences( m2, 
  disorder = "bipolar disorder" )
head(sentences$PUBMED_ID)

## ----jaccard_1, warning=FALSE-------------------------------------------------
xx <- jaccardEstimation( genesOfInterest, "bipolar disorder", 
  database = "ALL", nboot = 500 )
xx

## ----jaccard_2----------------------------------------------------------------
extract( xx )

## ----jaccard_3, warning=FALSE-------------------------------------------------
xx <- jaccardEstimation( genesOfInterest, 
  database = "ALL", nboot = 500 )

## ----jacc, fig.cap="Bar-plot where the Jaccard Index of each comparison between the list of genes of interest and PsyGeNET's diseases is shown.", fig.wide = TRUE----
plot( xx )

## ----bpGenes, fig.cap="Barplot: Genes associated to each of the psychiatric disorders", fig.wide = TRUE----
geneAttrPlot( m1, type = "disease category" )

## ----bpDis, fig.cap="Barplot: CUIs and psychiatric categories associated to each gene", fig.wide = TRUE----
geneAttrPlot( m1, type = "gene" )