formatReactome {ENVISIONQuery} | R Documentation |
Convert the EnXML PICR service results file into the protein interaction data frame
formatReactome(xml, filter=list(), compact=TRUE, verbose=TRUE)
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. |
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.
Alex Lisovich, Roger Day