Interface to Colombos Compendia using the Exposed REST API

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Documentation for package ‘Rcolombos’ version 2.0.2

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Rcolombos-package Interface to Colombos Compendia using the Exposed REST API
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.
advanced_search_by_both Accessory function allowing the advanced_search by both g_ids and c_ids
advanced_search_by_contrasts Accessory function allowing the advanced_search by contrast_ids, go, experiment, condition
advanced_search_by_genes Accessory function allowing the advanced_search by gene_ids, go, annotation
getCompendium This method allows to download/import the full compendium for the selected organism
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
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.
listContrasts This method takes as parameter a single string, representing an organism, and returns a character vector corresponding to the currently available organisms.
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
listGenes This method takes as parameter a single string, representing an organism, and returns a character vector corresponding to the currently available organisms.
listOrganisms Returns a character vector corresponding to the currently available organisms.
parseCompendium This method allows importing the full compendium for the selected organism from a local file
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
switchVersion Select the COLOMBOS REST API version to be used for retrieving data