formatReactome: Convert the EnXML PICR service results file into the protein...

In ENVISIONQuery: Retrieval from the ENVISION bioinformatics data portal into R

Description

Convert the EnXML PICR service results file into the protein interaction data frame

Usage

formatReactome(xml, filter=list(), compact=TRUE, verbose=TRUE)

Arguments

xml	Character string representing an Enfin xml file
filter	The list where the name of each element represents an output data frame column on which filetering is to be performed ('organism.species', 'Microarray.platform' etc.) and the element itself containing a character vector defining the set of values on which the merging (intersection) for a given column will be performed ('Homo sapiens' for 'organism.species', 'affy_hg_u133_plus_2' for 'Microarray.platform' etc.). The filtering is performed if the list is not empty and the formatIt=TRUE. Default is an empty list.
compact	If TRUE, collapses the rows with duplicated match sets but different attributes into a single row with unique match set and an attribute list separated by comma for each attribute column. Default is TRUE.
verbose	if TRUE enables diagnostic messages. Default is FALSE.

Value

The data frame with at least three columns, containing the source ID set, the pathway description and the link to Reactome web page for a given pathway correspondingly. If 'enfin-reactome-add-coverage' option is set to 'true' then two extra columns are added: for pathway coverage number, and total protein count per pathway.

Author(s)

Alex Lisovich, Roger Day

ENVISIONQuery documentation built on Nov. 8, 2020, 5:25 p.m.