calcGC: Calculate GC percent

Description Usage Arguments Value Author(s) See Also Examples

Description

Function to calculate GC percent from a nucleotide sequence input

Usage

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calcGC(x, ...)

Arguments

x

characters containing nucleotide sequence (ex: "ATCGGAA") or an object of class ExpressionSet

...

Other arguments passed to methods:

allow

vector of characters specifying what other characters to allow in sequence (default is "N")

Value

Returns a numerical value (from 0 to 1) indicating the C+G content of the sequence, corresponding to the fraction of (C+G)/(A+T+C+G...). A value of NA is returned if the function encounters an error that prevents proper calculation of GC percent.

Author(s)

Reid F. Thompson ([email protected])

See Also

calcGC-methods, calcTm

Examples

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#demo(pipeline,package="HELP")

calcGC("AAAACGCG")
calcGC(sequence="cXgXcXgXcXgX",allow="X")

HELP documentation built on Nov. 1, 2018, 3:34 a.m.