identifier: Queries for one or multiple identifiers

Description Usage Arguments Details Value Examples

Description

Analyse the post identifiers over the different species or projects the result to Homo Sapiens

Usage

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Arguments

id

character vector. one or multiple identifiers to analyse followed by their expresssion(when applied)

file

path to file that contains data to be analysed.

MakeProjection

logical, whether projects the result to Homo Sapiens or not.

IncludeInteractors

logical. whether include interactors.

pageSize

integer. pathways per page.

page

integer. page number

sortBy

string. how to sort the result.

order

string. specifies the order.

resource

string. the resource to sort.

silent

logical, to run quietly.

Details

The projection is calculated by the orthologous slot in the Reactome database. Use page and pageSize to reduce the amount of data retrieved. Use sortBy and order to sort the result by your preferred option. The resource field will filter the results to show only those corresponding to the preferred molecule type (TOTAL includes all the different molecules type).

sortBy can be one of NAME,TOTAL_ENTITIES,TOTAL_INTERACTORS, TOTAL_REACTIONS,FOUND_ENTITIES,FOUND_INTERACTORS,FOUND_REACTIONS,ENTITIES_RATIO, ENTITIES_PVALUE,ENTITIES_FDR,REACTIONS_RATIO.

order can be ASC or DESC.

resource can be TOTAL,UNIPROT,ENSEMBL,CHEBI,MIRBASE,NCBI_PROTEIN, EMBL,COMPOUND.

Value

a list with a data frame including pathway information and the token object; if no pathway found, only a summary data frame will be returned.

The summary.token can be used to retrieve the results of a previously performed analysis without the need to submit the sample again.

Examples

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# analyse multiple ids at the same time
pathwayInf.1 = rtAnalyseIdentifier(id = c('PTEN', 'PIK3C2A', 'UNC58'))
# projects the result to Homo Sapiens
pathwayInf.2 = rtAnalyseIdentifier(id = c('PTEN', 'PIK3C2A', 'UNC58'),
MakeProjection = TRUE)

VonWebEinstein/ReactomeAPI documentation built on May 9, 2019, 10:02 p.m.