computeNodeOverrep: Perform overrepresentation analysis on the input entities
In kwanjeeraw/metabox: metabox

Description Usage Arguments Details Value Author(s) References See Also Examples

perform overrepresentation analysis using hypergeometric tests to retrieve overrepresented annotation terms of the input entities.

1	computeNodeOverrep(txtinput, nodetype, annotation, internalid, size)

`txtinput`	a character vector of entities e.g. c('pubchemId1', 'pubchemId2'). The value can be neo4j ids or grinn ids, see details and see `convertId` for how to convert ids. For Mesh annotation, PubChem CIDs are required.
`nodetype`	a string specifying a node type. It can be one of compound (default), protein, gene, pathway, rna, dna.
`annotation`	a string specifying the annotation type e.g. pathway (default) and mesh. Pathway annotation requires the database. Mesh annotation doesn't require the database but it is available for PubChem compounds only.
`internalid`	a logical value indicating whether `txtinput` is the neo4j id, if TRUE (default). If not, `txtinput` is expected to be the grinn id or PubChem CID. See details and see `convertId` for how to convert ids. It has no effect on Mesh annotation.
`size`	a numeric vector specifying the minimum number of members in each annotation term to be used in the analysis. Default is 3.

The database uses two id systems. The neo4j id is a numeric, internal id automatically generated by the database system. The grinn id (gid) is an id system of Grinn database that uses main ids of standard resources i.e. ENSEMBL for genes (e.g.ENSG00000139618), UniProt for proteins (e.g.P0C9J6), PubChem CID for compounds (e.g.5793), KEGG for pathways (e.g.hsa00010).

list of data frame of nodes, edges and overrepresentation. The nodes data frame contains input attributes. The edges data frame contains annotation pairs. The data frame of overrepresentation contains the following components:

rank = rank sort by p adj

id = annotation id or annotation neo4j id

gid = annotation id or annotation grinn id

nodename = annotation name

nodelabel = annotation type

nodexref = cross references

p = raw p-values

p_adj = adjusted p-values

no_of_entities = number of input entities in each annotation term

annotation_size = total number of entities in each annotation term from the database

background_size = total number of annotated entities in the database

member = list of entity members of the annotation term

Return list of empty data frame if error or found nothing.

Kwanjeera W kwanich@ucdavis.edu

Johnson NL., Kotz S., and Kemp AW. (1992) Univariate Discrete Distributions, Second Edition. New York: Wiley.

phyper, p.adjust

1
2

#txtinput <- c(1110,10413,196,51,311,43,764,790) #compute overrepresented terms for given pubchem compounds
#result <- computeNodeOverrep(txtinput=txtinput, nodetype="compound", annotation="mesh", internalid=FALSE)

kwanjeeraw/metabox documentation built on May 20, 2019, 7:07 p.m.