Reactome Over-Representation or Expression Analysis
Using this function, you can perform Reactome Analysis In a convenient way. The Analysis Type will be chosen depending on your provided input:
If you provide a vector or a single-columned table, "Over-Representation" analysis will be performed.
If you provide a multi-column table, with the first column being molecules identifiers and the rest being numeral expression values, "Expression" analysis will be performed.
Refer to the details section for the accepted input types and format.
rba_reactome_analysis( input, input_format = NA, projection = FALSE, interactors = FALSE, species = NA, sort_by = "ENTITIES_PVALUE", order = "ASC", resource = "TOTAL", p_value = 1, include_disease = TRUE, min = NA, max = NA, ... )
input |
A vector, data frame, matrix or a local file path or URL that points to your data. See "Details section" for more information of how to organize and provide your input. |
input_format |
(Optional) This function will automatically identify your provided input's format. But in case of unexpected issues or if you want to be explicit, set this argument to one of:
|
projection |
Logical (default = FALSE) Should non-human identifiers be projected to their human equivalents? (using Reactome orthology data) |
interactors |
Logical (default = FALSE) Should IntAct interaction data be used to increase the analysis background? |
species |
Numeric or Character: NCBI Taxonomy identifier (Human
is 9606), species name (e.g. "Homo sapiens") or Reactome DbId (e.g
Homo sapiens is 48887). Refer to
|
sort_by |
Sort the result based on what column? available choices are: "NAME", "TOTAL_ENTITIES", "TOTAL_INTERACTORS", "TOTAL_REACTIONS", "FOUND_ENTITIES", "FOUND_INTERACTORS", "FOUND_REACTIONS", "ENTITIES_RATIO", "ENTITIES_PVALUE", "ENTITIES_FDR" or "REACTIONS_RATIO" |
order |
Sort Order. Can be either "ASC" (default) or "DESC". |
resource |
Filter results based on the resource. Default is "TOTAL", available choices are: "TOTAL", "UNIPROT", "ENSEMBL", "CHEBI", "IUPHAR", "MIRBASE", "NCBI_PROTEIN", "EMBL", "COMPOUND", "ENTITIES_FDR" or "PUBCHEM_COMPOUND". |
p_value |
Set a P value threshold. Only results with P value equal to or less than your provided threshold will be returned. (default = 1, Meaning no P value filtering) |
include_disease |
Logical (default = TRUE) Should the disease pathways be included in the results? |
min |
(numeric) Minimum number of entities that a pathways should have to be included in the results. |
max |
(numeric) Maximum number of entities that a pathways should have to be included in the results. |
... |
rbioapi option(s). Refer to |
You can provide your table or vector input in numerous formats:
A R object which can be data frame, matrix or a simple vector.
A path to a local text file in your device that contains the molecules data. (The file should be formatted correctly, see below.)
A URL pointing to a text file on the web that contains the molecules data. (The file should be formatted correctly, see below.
If you provide a text file (as a local file path or URL), it should be
in TSV (Tab-Separated Values) format; Column names should start with "#"
character. Note that if you are providing the file for
"Over-Representation" analysis (i.e. Single columned-data) this header
line is optional and will be used as your 'Sample Name', otherwise it is
required.
Also, form the "summary" element in the function's output, you can see
how Reactome Interpreted your input and subsequently the type of analysis
that has been performed.
There is no strict criteria about the type of your molecules Identifiers,
Reactome will Map the IDs to it's internal database entities.
Nevertheless, You can check if all your identifiers has been found in
"identifiersNotFound" element in the function's output.
After Any Analysis, Reactome will associate a token to your analysis.
It can be later used to in function that requires the token (e.g to retrieve
the analysis results, download pdf).
Note that Reactome will store your token for only 7 days. You can
download your full results with
rba_reactome_analysis_download, and re-import it anytime to
reactome (using rba_reactome_analysis_import) to generate
a new token.
List containing the results and information of your analysis. Note that you can use the token returned in the "summary" sub-list of the results (i.e. results$summary$token) to retrieve your results later or in other Reactome analysis functions.
"POST https://reactome.org/AnalysisService/identifiers/form"
"POST https://reactome.org/AnalysisService/identifiers/url"
"POST https://reactome.org/AnalysisService/identifiers/form/projection"
"POST https://reactome.org/AnalysisService/identifiers/url/projection"
Fabregat A, Sidiropoulos K, Viteri G, Forner O, Marin-Garcia P, Arnau V, D'Eustachio P, Stein L, Hermjakob H. Reactome pathway analysis: a high-performance in-memory approach. BMC bioinformatics. 2017 Mar;18(1) 142. doi: 10.1186/s12859-017-1559-2. PubMed PMID: 28249561. PubMed Central PMCID: PMC5333408.
Other "Reactome Analysis Service":
rba_reactome_analysis_download(),
rba_reactome_analysis_import(),
rba_reactome_analysis_mapping(),
rba_reactome_analysis_pdf(),
rba_reactome_analysis_species(),
rba_reactome_analysis_token()
rba_reactome_analysis(input = c("p53", "BRCA1", "cdk2", "Q99835", "CDC42"))
## Not run:
rba_reactome_analysis(input = "c:/rbioapi/genes.txt")
## End(Not run)
## Not run:
rba_reactome_analysis(input = "https://qazwsx.com/genes.txt")
## End(Not run)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.