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Rcolombos

Interface to COLOMBOS compendia using the exposed REST API.

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Version

Install

install.packages('Rcolombos')

Monthly Downloads

17

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)

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

This method allows to download/import the full compendium for the selected organism

Returns a character vector corresponding to the currently available organisms.

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

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.

Interface to Colombos Compendia using the Exposed REST API

This method takes a string containing the nickname for the selected organism and a string containing the annotation type and return the available entities

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.

This method takes as parameter a single string, representing an organism, and returns a character vector corresponding to the currently available organisms.