env.extract {ptm} | R Documentation |
Sequence Environment Around a Given Position
Description
Extracts the sequence environment around a given position.
Usage
env.extract(prot, db = 'none', c, r, ctr = 'none', exclude = c())
Arguments
prot |
either a uniprot id or a string sequence. |
db |
a character string specifying the desired database; it must be one of 'uniprot', 'metosite', 'none'. |
c |
center of the environment. |
r |
radius of the environment. |
ctr |
the type of control environment; it must be one of 'random', 'closest', or 'none'. |
exclude |
a vector containing the positions to be excluded as control. |
Details
The random control returns an environment center at a random position containing the same type or amino acid than the positive environment. The closest control searches for the closest position where such a type of amino acid is found and returns its environment.
Value
Returns a list of two strings (environments).
Author(s)
Juan Carlos Aledo
References
Aledo et al. Sci Rep. 2015; 5: 16955. (PMID: 26597773)
See Also
env.matrices(), env.Ztest() and env.plot()
Examples
env.extract('P01009', db = 'uniprot', 271, 10, ctr = 'random')