getGeneInfoByPapers: Get gene information for set of genes mentioned by certain...

In lptolik/synaptome.db: Synamptosome Proteome Database

Get gene information for set of genes mentioned by certain papers.

Description

Function lookup for specified PubMedIDs in the gene reference data and return following features for genes referenced by requested papers at least cnt times: GeneID (internal database ID), Localisation (one of the following: presynaptic, postsynaptic, synaptosome), MGI (MGI ID), HumanEntrez (Human Entrez ID), MouseEntrez (Mouse Entrez ID), HumanName (Human gene name), MouseName (Mouse gene name), PaperPMID (PMID IDs for the publications where the genes were reported if it is within pmids list), Paper (papers where specific genes were reported in a format FIRSTAUTHOR_YEAR), Year, SpeciesTaxID (specie the original experiment was performed on), BrainRegion (Brain region where the specific genes were identified, according to the paper)

Usage

getGeneInfoByPapers(pmids, cnt = 1)

Arguments

pmids	vector of PMIDs to search for genes
cnt	minimal number of papers that mentioned gene

Details

This function then returns following features for all found genes:

• GeneID,

• Localisation,

• MGI,

• HumanEntrez,

• MouseEntrez,

• HumanName,

• MouseName,

• PaperPMID,

• Paper,

• Year,

• SpeciesTaxID,

• BrainRegion

Value

data.frame with fields specified above.

See Also

Other GeneInfo functions: getGeneInfoByEntrez(), getGeneInfoByIDs(), getGeneInfoByName()

Examples

res<- getAllGenes4Compartment(compartmentID = 1)
gnt<-getGeneInfoByIDs(res$GeneID)
pmids<-names(sort(table(gnt$PaperPMID))[1:5])
cntT <- getGeneInfoByPapers(pmids,cnt=3)
head(cntT)

lptolik/synaptome.db documentation built on Sept. 13, 2023, 2:50 p.m.