Package 'psygenet2r'

Title: psygenet2r - An R package for querying PsyGeNET and to perform comorbidity studies in psychiatric disorders
Description: Package to retrieve data from PsyGeNET database (www.psygenet.org) and to perform comorbidity studies with PsyGeNET's and user's data.
Authors: Alba Gutierrez-Sacristan [aut, cre], Carles Hernandez-Ferrer [aut], Jaun R. Gonzalez [aut], Laura I. Furlong [aut]
Maintainer: Alba Gutierrez-Sacristan <[email protected]>
License: MIT + file LICENSE
Version: 1.37.0
Built: 2024-06-30 03:35:51 UTC
Source: https://github.com/bioc/psygenet2r

Help Index

Class DataGeNET.Psy

Description

Class DataGeNET.Psy is the basic object use in psygenet2r package. It is the main data container to using the different functions to query PsyGeNET database and generate teir output. The constructors of this class are the functions psygenetGene and psygenetDisease.

Slots

type

Character containing 'gene' of 'disease'. It is used to eprform the correct query to PsyGeNET.

search

Character containing 'single' of 'list'.It is used to eprform the correct query to PsyGeNET.

database

Character containing the name of the database that will be queried. It can take the values 'MODELS' to use Comparative Toxigenomics Database, data from mouse and rat; 'GAD' to use Genetic Association Database; 'CTD' to use Comparative Toxigenomics Database, data from human; 'PsyCUR' to use Psychiatric disorders Gene association manually curated; 'CURATED' to use Human, manually curated databases (PsyCUR and CTD); or 'ALL' to use all these databases.

term

Charcter with the term(s) to search into the database(s).

qresult

data.frame with the obtained result

See Also

psygenetGene, psygenetDisease, DataGeNET.Psy-methods

Enrichment of a user's input (genes) in PsyGeNET's diseases.

Description

Test the enrichment of a given gene list on Psychiatric Disorders from PsyGeNET.

Usage

enrichedPD(gene, database = "ALL", verbose = FALSE, warnings = FALSE)

Arguments

gene

Name or vector of names (that can be both code or uml) to specific genes from PsyGeNET.
database

Name of the database that will be queried. It can take the values 'psycur15' to use data validated by experts for first release of PsyGeNET; 'psycur16' to use data validated by experts for second release of PsyGeNET; or 'ALL' to use both databases. Default 'ALL'.
verbose

By default FALSE. Change it to TRUE to get a on-time log from the function.
warnings

By default TRUE. Change it to FALSE to not see the warnings.

Value

A data.frame with the enricment at each Psychiatric Disorder

Examples

enrichedPD(c("ADCY2", "AKAP13", "ANK3"), "ALL")

Raw data from DataGeNET.Psy and JaccardIndexPsy.

Description

Obtain the raw data from a PsyGeNET's query stored in a DataGeNET.Psy object or the raw data with all the Jaccard Index for the disease of interest of an JaccardIndexPsy object.

Usage

extract(object, ...)

## S4 method for signature 'DataGeNET.Psy'
extract(object)

## S4 method for signature 'JaccardIndexPsy'
extract(object, order.cl = "pval", ...)

Arguments

object

Object of class DataGeNET.Psy or JaccardIndexPsy
...

NO USED
order.cl

Order resulting data.frame by the name of this column.

Value

A data.frame containing the raw result from PsyGeNET or a data.frame with the result Jaccard Index for each disease.

A data.frame containing the raw result from PsyGeNET

A data.frame with the result Jaccard Index for each disease.

Methods (by class)

  • DataGeNET.Psy: Extract function for DataGeNET.Psy

  • JaccardIndexPsy: Extract function for JacardIndexPsy

Examples

data(qr)
extract(qr)[1:2, ] # get internat data.frame
## Not run: 
#Being x an JaccardIndexPsy
extract(x)

## End(Not run)

Method to obtain the sentences that support a gene-disease association from a DataGeNET.Psy object.

Description

PsyGeNET contains a list of sentences that support a gene-disease association from public literature. The internal table of a DataGeNET.Psy object contains this information. The method extractSentences allows to extract those sentences that support a gene-disease association given a DataGeNET.Psy object and a disorder of interest.

Usage

extractSentences(object, disorder, verbose)

## S4 method for signature 'DataGeNET.Psy'
extractSentences(object, disorder, verbose = FALSE)

Arguments

object

Object of class DataGeNET.Psy.
disorder

The disorder of interest. Only those sentences supporting a gene-disease association with this specific disorder will be extracted. Disorder must be provided by using "Disease Id" or "Disease Name". The "Disease Id" can be provided with or without the "uml" tag. Example of a "Disease Name": "schizophrenia"; Example of a "Disease Id": "umls:C0036341", that is equivalent of using "C0036341".
verbose

If set to TRUE informative messages are show.

Value

A data frame showing the sentences.

Methods (by class)

  • DataGeNET.Psy: Get sentences or evidences

Examples

data(qr)
extractSentences(qr, "Depression")

Ploting the relation between genes and disease-categories

Description

Given a set of genes or a result of psygenetGene creates four types of plots showing the relation of the genes with the disease's category in psyGeNET.

Usage

geneAttrPlot(x, type = "pie", ..., verbose = FALSE)

Arguments

x

Vector of genes of interest of DataGeNET.Psy resulting of psyegnetDisease.
type

Type of the drawn chart. By default it is "pie". It can takes "pie" to plot a pie chart with the number of genes for each psychiatric category, "disease category" for visualizing a barplot with the total and specific number of genes for each psychiatric disorder, "evidence index" for a barplot showing for each psychiatric disorder the number of gene-disease associations according to the Evidence index and "gene" for visualizing a barplot with the total and specific number of diseases associated to each gene.
...

(Check NOTE section) Passed to inner functions for different plots.
verbose

By default FALSE. Change it to TRUE to get a on-time log from the function.

Value

A plot for a DataGeNET.Psy in terms of the panther-class.

Note

The "Evidence Index" is gotten from PsyGeNET. For more information about it and its calculation, pease visit psygenet.org. Argument ... can be filled with specific argument depending on the type of plot:

Type Argument Color Description
gene cuiBarColor Purple Determines the color of the bar for diseases
diseaseCategoryBarColor Yellow Determines the color of the bar for psychiatric categories
disease category uniqueGenesBarColor Orange Determines the color of the bar for unique genes for a disease category
totalGenesBarColor Blue Determines the color of the bar for total genes for a disease category

Query PsyGeNET for given gene(s) and generates an DataGeNET.Psy

Description

Given the name of one or multiple gene and retrives their information from PsyGeNET and creates an object of type DataGeNET.Psy.

Usage

getUMLs(word, database = "ALL")

Arguments

word

Disese to convert to UMLS using PsyGeNET database.
database

Name of the database that will be queried. It can take the values 'psycur15' to use data validated by experts for first release of PsyGeNET; 'psycur16' to use data validated by experts for second release of PsyGeNET; or 'ALL' to use both databases. Default 'ALL'.

Value

The corresponding UMLs for the input disease/s

Examples

umls <- getUMLs( word = "depressive", database = "ALL" )

Calculation of the Jaccard Index between ideseases

Description

This function is able to calculate the Jacard Index between: 1. muliple disases, 2. a set og genes and multiple diseases, 3. a set of genes and multiple main psychiatric disorders and 4. multiple diseases and multiple main psychiatric disorders.

Usage

jaccardEstimation(pDisease, sDisease, database = "ALL", nboot = 100,
  ncores = 1, verbose = FALSE)

Arguments

pDisease

vector of diseases, vector of genes, vector of main psychiatric disorder.
sDisease

vector of diseases, vector of genes, vector of main psychiatric disorder. Only necessary when comparing genes vs. diseases, genes vs. main psychiatric disorders or diseases vs. main psychiatric disorders. To compare multiple diseases only use pDisease.
database

Name of the database that will be queried. It can take the values 'psycur15' to use data validated by experts for first release of PsyGeNET; 'psycur16' to use data validated by experts for second release of PsyGeNET; or 'ALL' to use both databases.
nboot

Number of iterations sued to compute the pvalue associted to the calculated Jaccard Index (default 100).
ncores

Number of cores used to calculate the pvalue associated to the computed Jaccard Index (default 1).
verbose

By default FALSE. Change it to TRUE to get a on-time log from the function.

Details

Warning: The main psychiatric disorders are understood as a single set of genes composed by the genes of all the diseases that the main psychiatric disorder cotains.

Value

An object of class JaccardIndexPsy with the computed calculation of the JaccardIndex.

Examples

ji <- jaccardEstimation( c( "COMT", "CLOCK", "DRD3" ), "umls:C0005586", "ALL" )

Class JaccardIndexPsy

Description

Class JaccardIndexPsy is theresult of the process to look for a Jaccard Index between muliple diseases in psygenet2r package.

Slots

nit

Number of iterations to calculate the estimated Jaccard index

type

Slot to save type of query (disease-disease, gene-disease)

table

data.frame containing the result table of Jaccard indexes

i1

[internal use] vector with names of first component

i2

[internal use] vector with names of second component

See Also

psygenetGene, psygenetDisease, JaccardIndexPsy-methods

Examples

ji <- jaccardEstimation( c( "COMT", "CLOCK", "DRD3" ), "umls:C0005586", "ALL" )

Getter from DataGeNET.Psy.

Description

Obtain the number of unique diseases in a DataGeNET.Psy.

Usage

ndisease(object)

## S4 method for signature 'DataGeNET.Psy'
ndisease(object)

Arguments

object

Object of class DataGeNET.Psy.

Value

The number of unique diseases

Methods (by class)

  • DataGeNET.Psy: Get number of diseases

Examples

data(qr)
ndisease(qr)

Getter from DataGeNET.Psy.

Description

Obtain the number of unique genes in a DataGeNET.Psy.

Usage

ngene(object)

## S4 method for signature 'DataGeNET.Psy'
ngene(object)

Arguments

object

Object of class DataGeNET.Psy.

Value

The number of unique genes

The number of unique genes

Methods (by class)

  • DataGeNET.Psy: Get number of genes

Examples

data(qr)
ngene(qr)

Query PsyGeNET for given genes and creates a representation in base of their panther-class

Description

Given a vector of genes of interest (or using a DataGeNET.Psy object), this function creates a representation of a the panther-class these genes belongs to.

Usage

pantherGraphic(x, database = "ALL", evidenceIndex, verbose = FALSE)

Arguments

x

Vector of genes of interest of DataGeNET.Psy resulting of psyegnetDisease.
database

Name of the database that will be queried. It can take the values 'psycur15' to use data validated by experts for first release of PsyGeNET; 'psycur16' to use data validated by experts for second release of PsyGeNET; or 'ALL' to use both databases. Default 'ALL'.
evidenceIndex

threshold to take into account a gene in the analysis
verbose

By default FALSE. Change it to TRUE to get a on-time log from the function.

Value

A plot for a DataGeNET.Psy in terms of the panther-class.

Examples

d.alch <- pantherGraphic( c( "COMT", "CLOCK", "DRD3" ), "ALL" )

Plots the content of a DataGeNET.Psy object

Description

This functions llows to create a variety of plots for DataGeNEt.Psy and JaccardIndexPsy objects.

Usage

## S4 method for signature 'DataGeNET.Psy,ANY'
plot(x, y,
  layout = igraph::layout.fruchterman.reingold, type = "GDA network",
  verbose = FALSE, ...)

Arguments

x

Object of class DataGeNET.Psy
y

NOT USED
layout

Function to design the location of the different nodes. By default layout.fruchterman.reingold from igraph is used.
type

Type of the drawn chart. By default it is "GDA network" but it also can be "GDCA network", "GDCA heatmap", "GDA heatmap" and "publications". The first two are network representations of the second two. While the last one draws a barplot with the number of PMIDs between genes and diseases.
verbose

By default FALSE. If set to TRUE information on the drawing process will be shown.
...

(Check NOTE section) Passed to inner functions for different plots.

Value

A plot for DataGeNET.Psy.

Note

The "Evidence Index" is gotten from PsyGeNET. For more information about it and its calculation, pease visit psygenet.org. Argument ... can be filled with specific argument depending on the type of plot:

Type Argument Color Description
GDA network geneColor Yellow Determines the color of the gene nodes
diseaseColor Blue Determines the color of the disease nodes
GDA heatmap highColor Blue Determines the color of the heatmap for the highest value
lowColor White Determines the color of the heatmap for the lowest value
GDCA network ei0color Yellow Determines the color for those associations with evidence index 0
eiAmbiguitcolor Grey Determines the color for those associations with evidence index greater than 0 and lower than 1
ei1color Blue Determines the color for those associations with evidence index 1
GDCA heatmap AUDcolor #FF3C32
BDcolor #FFC698
DEPcolor #9BE75E
SCHZcolor #1F6024
CUDcolor #5AB69C
SIDEPcolor #50B8D6
CanUDcolor #5467C3
SYPSYcolor #A654C3
geneColor Orange

Examples

data(qr)
plot(qr) # for all-disease plot
plot(qr, type = 'GDCA network') # for MPI plot

Plot the content of a JaccardIndexPsy object.

Description

This functions llows to create a variety of plots for DataGeNEt.Psy and JaccardIndexPsy objects.

Usage

## S4 method for signature 'JaccardIndexPsy,ANY'
plot(x, y, cutOff, zero.remove = TRUE,
  noTitle = FALSE, lowColor = "white", highColor = "mediumorchid4",
  verbose = FALSE, ...)

Arguments

x

Object of class JaccardIndexPsy.
y

NOT USED
cutOff

Number to filter the shown results.
zero.remove

By deffault TRUE. It removes those relations with a Jaccard Index of 0.
noTitle

By default FALSE. If set to true no title will be added to the plot.
lowColor

By default "white". It can be changed to any other color.
highColor

By default "mediumorchid4". It can be changed to any other color.
verbose

By default FALSE. If set to TRUE information on the drawing process will be shown.
...

NOT USED

Value

A plot for JaccardIndexPsy.

Examples

## Not run: 
#Being x an JaccardIndexPsy
qr <- plot(x)

## End(Not run)

psygenet2r: Package to query PsyGeNET database and to perform comorbidity studies

Description

psygenet2r has two categories of functions: querying functions and analysis and plotting functions.

querying functions

The functions to retrieve data from PsyGeNET are psygenetDisease and psygenetGene. There are some other support functions like psygenetGeneSentences.

analysis and plotting functions

The functions extract and extractSentences allows to retrieve the row data obtained from on-line resources. The functions plot and pantherGraphic draws a variety of charts to illustrate the obtained results. The function enrichedPD was built to perform enrichment studies on PsyGeNET data. Finally the function jaccardEstimation computes a Jaccard Index from a given input on PsyGeNET data.

Query PsyGeNET for given disease(s) and generates an DataGeNET.Psy

Description

Given the name of one or multiple diseases and retrives their information from PsyGeNET and creates an object of type DataGeNET.Psy.

Usage

psygenetDisease(disease, database = "ALL", evidenceIndex = c(">", 0),
  verbose = FALSE, warnings = TRUE)

Arguments

disease

Name or vector of names (that can be both code or uml) to specific diseases from PsyGeNET. The diseases non existing in PsyGeNET will be removed from the output.
database

Name of the database that will be queried. It can take the values 'psycur15' to use data validated by experts for first release of PsyGeNET; 'psycur16' to use data validated by experts for second release of PsyGeNET; or 'ALL' to use both databases. Default 'ALL'.
evidenceIndex

A vector with two elements: 1) character with greather '>' or with lower '<' meaing greather or equal and lower or equal; 2) the evidence index cut-off to be compared. By default: c('>', 0).
verbose

By default FALSE. Change it to TRUE to get a on-time log from the function.
warnings

By default TRUE. Change it to FALSE to don't see the warnings.

Value

An object of class DataGeNET.Psy

Note

The "Evidence Index" is gotten from PsyGeNET. For more information about it and its calculation, pease visit psygenet.org.

Examples

d.sch <- psygenetDisease( "schizophrenia", "ALL" )

Query PsyGeNET for given disease(s) and extract the pmids sentences that report a gene-disease asssociation.

Description

Given a disease or a disease list, retrives the pmids and sentences for each gene-disease association from PsyGeNET and creates an object of type DataGeNET.Psy.

Usage

psygenetDiseaseSentences(diseaseList, database = "ALL", verbose = FALSE)

Arguments

diseaseList

Name or vector of names (that can be both code or uml) to specific diseases from PsyGeNET. The diseases non existing in PsyGeNET will be removed from the output.
database

Name of the database that will be queried. It can take the values 'psycur15' to use data validated by experts for first release of PsyGeNET; 'psycur16' to use data validated by experts for second release of PsyGeNET; or 'ALL' to use both databases. Default 'ALL'.
verbose

By default FALSE. Change it to TRUE to get a on-time log from the function.

Value

An object of class DataGeNET.Psy

Examples

diseasesOfInterest <- c( "Bipolar Disorder","Depressive Disorder, Major" )
psyDisSen <- psygenetDiseaseSentences( diseaseList = diseasesOfInterest,
                                       database = "ALL" )

Query PsyGeNET for given gene(s) and generates an DataGeNET.Psy

Description

Given the name of one or multiple gene and retrives their information from PsyGeNET and creates an object of type DataGeNET.Psy.

Usage

psygenetGene(gene, database = "ALL", evidenceIndex = c(">", 0),
  verbose = FALSE, warnings = TRUE)

Arguments

gene

Name or vector of names (that can be both code or symbol) to specific genes from PsyGeNET. The genes non existing in PsyGeNET will be removed from the output.
database

Name of the database that will be queried. It can take the values 'psycur15' to use data validated by experts for first release of PsyGeNET; 'psycur16' to use data validated by experts for second release of PsyGeNET; or 'ALL' to use both databases. Default 'ALL'.
evidenceIndex

A vector with two elements: 1) character with greather '>' or with lower '<' meaing greather or equal and lower or equal; 2) the evidence index cut-off to be compared. By default: c('>', 0).
verbose

By default FALSE. Change it to TRUE to get a on-time log from the function.
warnings

By default TRUE. Change it to FALSE to not see the warnings.

Value

An object of class DataGeNET.Psy

Note

The "Evidence Index" is gotten from PsyGeNET. For more information about it and its calculation, pease visit psygenet.org.

Examples

d.alch <- psygenetGene( "ALDH2", "ALL" )

Query PsyGeNET for given gene(s) and extract the pmids sentences that report a gene-disease asssociation.

Description

Given a gene or a gene list, retrives the pmids and sentences for each gene-disease association from PsyGeNET and creates an object of type DataGeNET.Psy.

Usage

psygenetGeneSentences(geneList, database = "ALL", verbose = FALSE)

Arguments

geneList

Name or vector of names (that can be both code or symbol) to specific genes from PsyGeNET. The genes non existing in PsyGeNET will be removed from the output.
database

Name of the database that will be queried. It can take the values 'psycur15' to use data validated by experts for first release of PsyGeNET; 'psycur16' to use data validated by experts for second release of PsyGeNET; or 'ALL' to use both databases. Default 'ALL'.
verbose

By default FALSE. Change it to TRUE to get a on-time log from the function.

Value

An object of class DataGeNET.Psy

Examples

genesOfInterest <- c("PECR", "ADH1C", "CAST", "ERAP1", "PPP2R2B",
                     "ESR1", "GATA4", "CDH13")
psyGeneSen <- psygenetGeneSentences( geneList = genesOfInterest,
                                     database = "ALL")

DataGeNET.Psy obtained from quering PsyGeNET for gene '4852'.

Description

A dataset obtained from PsyGeNET after being queried with psygenetGene usig the term '4852' on "ALL" database.

Usage

data("qr")

Format

The format is: Formal class 'DataGeNET.Psy' [package "psygenet2r"] with 5 slots .. type : chr "gene" .. search : chr "" .. database: chr "ALL" .. term : chr "4852" .. qresult :'data.frame'

Value

A DataGeNET.Psy object.

Source

http://psygenet.org

Examples

ngene(qr)
ndisease(qr)

Enrichment of a user's input (genes) in anatomical terms (TopAnat).

Description

Test the enrichment of a given gene list on Psychiatric Disorders from PsyGeNET.

Usage

topAnatEnrichment(gene, datatype = c("rna_seq", "affymetrix", "est",
  "in_situ"), statistic = "fisher", cutOff = 1, verbose = FALSE,
  warnings = FALSE)

Arguments

gene

Name or vector of names (that can be both code or uml) to specific genes from PsyGeNET.
datatype

It can take the values 'rna_seq', 'affymetrix', "est" or "in situ". Default c("rna_seq","affymetrix","est","in_situ").
statistic

By default it is "fisher". But it can be changed to "ks", "t", "globaltest", "sum" or "ks.ties". All from runTest.
cutOff

Default 1.
verbose

By default FALSE. Change it to TRUE to get a on-time log from the function.
warnings

By default TRUE. Change it to FALSE to not see the warnings.

Value

A data.frame with the enrichment results

Examples

## Not run: 
topAnatEnrichment(gene=c("ADCY2", "AKAP13", "ANK3"))

## End(Not run)

Vector with gene universe for Jaccard Index

Description

Vector with all the gene names from DisGeNET database (http://www.disgenet.org) used as gene universe for Jaccard Index computation.

Usage

universe

Format

An object of class character of length 8947.

Details

data("universe", package = "psygenet2r")

Value

A character vector.

Source

http://www.disgenet.org

Examples

length(universe)
universe[1:10]