ENVISIONQuery.chunk: Retrieves a set of unique matches for a given ID list.

Description Usage Arguments Value Author(s)

View source: R/ENVISIONQuery.R

Description

Retrieves a set of unique matches for a given ID list.

Usage

1
2
3
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.

service

Service handler

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 <name,value> 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.

...

additional arguments.

Value

The ENVISIONQueryResult structure

Author(s)

Alex Lisovich, Roger Day


ENVISIONQuery documentation built on Nov. 1, 2018, 4:26 a.m.