getEpitope-methods: query Epitopes from HIV feature database

In RGLab/HIV.db: HIV Annotation

Description

The methods provide the interfaces to query the HIV feature database for Epitopes

Value

signature(object = "environment") and signature(object = "HivFeature") returns a Epitope object, signature(object = "list") returns a list of Epitope objects

Methods

signature(object = "environment")

Query the Epitopes directly from the data source stored in the environment. arguments are:

name:

a character that passes the feature name

species:

a character that passes the species information

start,end:

integers that passe the coordinates of the annotation on the HIV genome

frame:

an integer passes the frame number

Usage:

getEpitope(object,start=NULL,end=NULL,name=NULL,species=NULL,frame=NULL)

signature(object = "HivFeature")

This method perform the same kind of query as the first one and use the start,end coordinates of the HivFeature object as the extra query condition. Usage:

getEpitope(object,start=NULL,end=NULL,...)

start,end:

the coordinates of the HXB2 genome that intersect with coordinates of the HiveFeature object.

...:

additional arguments passed to getEpitope(object = "HivFeature") method

signature(object = "list")

This method takes a list of HivFeature objects as the input Usage:

getEpitope(object,...) ... are the arguments passed to getEpitope(object = "HivFeature") method

Author(s)

Mike Jiang,Raphael Gottardo

See Also

getFeature

Examples

library(HIV.db)

## load Table from db
HIV_db<-loadFeatures()
getEpitope(HIV_db,start=4240,end=5096,species="mouse",name="4D6",frame=3)

RGLab/HIV.db documentation built on May 8, 2019, 5:51 a.m.