getFeature: query the annotation feature from the HIV feature database

In RGLab/HIV.db: HIV Annotation

Description

The method provides the simply query interface to the HIV feature database

Value

A HivFeature object or a list of HivFeature objects

Methods

signature(object = "environment")

object is an environment that stores the HIV feature database, ...:

are the additional arguments:

name:

a character that stores the annotation name

category:

a character that stores the annotation category

start,end:

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

frame:

an integer storing the frame number of the annotation

Usage:

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

Author(s)

Mike Jiang,Raphael Gottardo

See Also

getEpitope, HivFeature

Examples

library(HIV.db)

## load Table from db
HIV_db<-loadFeatures()
## query by name or category
getFeature(HIV_db, category=c("gene"))
getFeature(HIV_db, category=c("gene"),frame=3)
getFeature(HIV_db, name=c("gp120","gp41"))
getFeature(HIV_db, category="loop")

## query by hxb2 coordinates
getFeature(HIV_db,start=7100,end=7200)
getFeature(HIV_db,start=6225,end=8795)

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