Usage
ENVISIONQuery.chunk(ids, utilityTool, service, tool, formatIt, options=list(), filter=list(), compact=TRUE, writeHTML=FALSE, nchunk=NA, verbose=FALSE, ...)
Arguments
ids
Character vector representing the ID list.
utilityTool
The tool used to convert the ID list into the input Enfin xml file.
tool
The tool used to perform the conversion
formatIt
If TRUE (default), try to interpret the returned character table and structure the result.
If false, the character string representing the entire enfinXML file returned by ENVISION.
options
The (optional)list each element of which represents the pair used to apply
the additional constraints when sending a query to a particular service (maximum number of pathways
for Reactome service as an example)
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 and the formatted output (formatIt = TRUE)is represented by a data frame,
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.
writeHTML
If TRUE, write the received intermediate HTML to file. Default is FALSE.
nchunk
Chunk number. If not NA and writeHTML is TRUE the input and output xml file names are appended
with chunk number. Default is NA.
verbose
If TRUE, enables diagnostic messages. Default is FALSE.