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Rcolombos
Interface to
COLOMBOS
compendia using the exposed REST API.
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2.0.2
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install.packages('Rcolombos')
Monthly Downloads
102
Version
2.0.2
License
GPL-3
Homepage
http://colombos.net/
Maintainer
Paolo Sonego
Last Published
November 2nd, 2015
Functions in Rcolombos (2.0.2)
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get_contrast_annotations
This method allows to retrieve all the annotations for the Reference and Test conditions for a selected organism (nickname) and for a user specified contrast name. Please be aware that only one contrast is allowed in input. It returns a list containing both ReferenceAnnnotation and TestAnnotation. and return the available entities
getCompendium
This method allows to download/import the full compendium for the selected organism
listOrganisms
Returns a character vector corresponding to the currently available organisms.
listContrasts
This method takes as parameter a single string, representing an organism, and returns a character vector corresponding to the currently available organisms.
listAnnotationTypes
This method takes as parameter a string (the nickname of an organism) and returns a character vector corresponding to the currently available annotation type for the selected organism.
parseCompendium
This method allows importing the full compendium for the selected organism from a local file
advanced_search_by_genes
Accessory function allowing the advanced_search by gene_ids, go, annotation
advanced_search_by_contrasts
Accessory function allowing the advanced_search by contrast_ids, go, experiment, condition
advanced_search_by_both
Accessory function allowing the advanced_search by both g_ids and c_ids
quick_search
This method mimics the quick_search functionality of Colombos. It takes a string containg the nickname for the selected organism and a vector of string representing the genes of interest for the specified organism and returns a list containing the locustags (gene_names), contrasts and M-values for the current selection.
Rcolombos
Interface to Colombos Compendia using the Exposed REST API
listEntities
This method takes a string containing the nickname for the selected organism and a string containing the annotation type and return the available entities
switchVersion
Select the COLOMBOS REST API version to be used for retrieving data
advanced_search
This method mimics the advanced_search functionality of Colombos. It takes a series of parameters, representing the different settings available on Colombos advanced search and returns a list containing the locustags (gene_names), contrasts and M-values for the current selection.
listGenes
This method takes as parameter a single string, representing an organism, and returns a character vector corresponding to the currently available organisms.