calculateMaxEntScanScore {VarCon}R Documentation

Calculate MaxEntScan score of a splice site sequence

Description

This function calculates the MaxEntScan score of either splice donor or acceptor sequences.

Usage

calculateMaxEntScanScore(seqVector, ssType)

Arguments

seqVector

Character vector of nucleotide sequence of a splice site sequences. SA sequences should be 23nt long (20 intronic, 3 exonic) and splice donor sequences should be 9nt long (3 exonic, 6 intronic) only contain bases "A", "G", "C", "T".

ssType

Numeric indicator, if the entred sequence is a splice donor (5) or acceptor (3)

Value

Character vector of the MaxEntScan scores generated from the entered seqVector.

Examples

calculateMaxEntScanScore("TTCCAAACGAACTTTTGTAGGGA",3)
calculateMaxEntScanScore("GAGGTAAGT",5)


[Package VarCon version 1.0.0 Index]