upstream: Find flanking features.

In biofiles: An Interface for GenBank/GenPept Flat Files

Description

Find flanking features.

Usage

upstream(query, subject, n = 5, include_key = "all", exclude_key = "none")

downstream(query, subject, n = 5, include_key = "all",
  exclude_key = "none")

flanking(query, subject, n = 5, include_key = "all", exclude_key = "none")

Arguments

query	A gbFeature or gbFeatureTable object.
subject	A gbRecord or gbFeatureTable object within which the n nearest upstream features are found.
n	The number of upstream features to be returned.
include_key	Which features should be returned. Defaults to “all”.
exclude_key	Which feature(s) should be excluded from the search. Defaults to “none”.

Value

A (list of) gbFeatureTables.

Examples

load(system.file("extdata", "S_cerevisiae_mito.rda", package = "biofiles"))
cytb <- ft(filter(x, product = "^cytochrome b$"))

## find the three nearest upstream neighbor CDS to CYTB 
upstream(cytb, x["CDS"], n = 3)

biofiles documentation built on May 2, 2019, 3:31 p.m.