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biofiles (version 1.0.0)

upstream: Find flanking features.

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

Run this code
# NOT RUN {
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)
# }

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