bbMapping: Chain mapping and filtering

In biobtreeR: Using biobtree tool from R

Description

Chain mapping identifiers or keywords with filtering and retrieving attributes if available.

Usage

bbMapping(terms, mapfilter, page = NULL, source = NULL, lite = TRUE,
  limit = 1000, inattrs = NULL, attrs = NULL,
  showInputColumn = FALSE)

Arguments

terms	Input terms for the mapping. Same with search functionality they can be comma seperated identifers or keywords
mapfilter	Mapping query which consist of map and optional filter functions in the form of map(dataset).filter(Boolean query expression) The boolean expressions are based on datasets attributes and dataset attributes can be list with bbAttr function. Dataset attributes which used in the filters starts with their dataset name. In biobtree boolean expressions feature has been implemented via Google common expression language so its full capability can be checked in its documentation.
page	Optional parameter works similar with bbSearch page paramter.
source	Optional dataset identifiers for searching input terms within the given dataset.
lite	By default it is TRUE and allow function return quickly with data.frame with mapping identifiers and attributes. If set to TRUE function return raw results converted from json.
limit	Limits the number of mapping results. By default without any limit all the results returned.
inattrs	Optional comma seperated attribute names for input identifiers and if available their values includes in result data.frame
attrs	Optional comma seperated attribute names for mapping identifiers and if available their values includes in result data.frame
showInputColumn	Optional logical parameter to show the input identifers in the result data.frame

Value

returns mapping results in data.frame by default if lite set it true returns json object

Author(s)

Tamer Gur

Examples

bbStart()

bbMapping("tpi1",'map(uniprot)')

bbMapping("shh",'map(ensembl)')

## Not run: 
# run these examples with building the default dataset with bbBuildData()
#Map protein to its go terms and retrieve go term types
bbMapping("AT5G3_HUMAN",'map(go)',attrs = "type")

#Map protein to its go terms with filter by its type and retrieve their types
bbMapping("AT5G3_HUMAN",'map(go).filter(go.type=="biological_process")',attrs = "type")

#Map gene names to exon identifiers and retrieve the region
bbMapping("ATP5MC3,TP53",'map(transcript).map(exon)',attrs = "seq_region_name")

#Map Affymetrix identifiers to Ensembl identifiers and gene names
bbMapping("202763_at,213596_at,209310_s_at",source ="affy_hg_u133_plus_2"
,'map(transcript).map(ensembl)',attrs = "name")


## End(Not run)

biobtreeR documentation built on Nov. 8, 2020, 5:19 p.m.