Description Usage Arguments Value Author(s)
Convert the EnXML IntAct service results file into the protein interaction data frame
1 | formatIntact(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 consisting of two groups of columns: the first containing the ID match set (i.e. 'Affymetrix GeneChip', 'Uniprot' etc.), and the second containing the attributes for a particular match ('organism.species', 'Microarray.Platform' etc.).
Alex Lisovich, Roger Day
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