identifySNPs: Identify SNPs
In MassArray: Analytical Tools for MassArray Data

Description Usage Arguments Details Value Author(s) Examples

Function to identify potential single nucleotide polymorphisms (SNPs) which allow mapping of a novel peak sequence to the expected amplicon sequence

1	identifySNPs(peak.sequence, sequence, rxn = c("T", "C"))

`peak.sequence`	Nucleotide sequence (can also be base composition - ex: "A6G2C1T3") as a character string
`sequence`	Nucleotide sequence for wildtype/expected amplicon as a character string
`rxn`	One of "T" or "C" specifying which cleavage reaction to use for SNP analysis

The algorithm steps through the sequence, substituting one nucleotide at a time with the other three base pairs or a blank character (deletion), in order to determine a base compositional match to the input peak.sequence which represents a peak not found in the native sequence.

Returns a list of potential SNP matches for the input peak.sequence. Each element of the list contains multiple items as follows:

`sequence`	corresponds to `peak.sequence`
`position`	corresponds to the matched position within `sequence`
`base`	corresponds to the altered nucleotide (i.e. "A", "T", "C", "G", or "")
`type`	corresponds to the class of SNP (i.e. "substitution" or "deletion")

Reid F. Thompson (rthompso@aecom.yu.edu), John M. Greally (jgreally@aecom.yu.edu)

## SINGLE SUBSTITUTION
identifySNPs("AAGT","AATTTT")
## MULTIPLE SUBSTITUTION POSSIBILITIES
identifySNPs("A1G1T1","AATTTT")
## DELETION
identifySNPs("AAT","AGATTTT")