Description Usage Arguments Details Value Examples
Analyse the post identifiers over the different species or projects the result to Homo Sapiens
1 2 3 |
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. |
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
.
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.
1 2 3 4 5 | # 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)
|
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