variantType: Get the type of variant given one or more reference alleles...

In chambm/customProDB: Generate customized protein databases from NGS data for proteomics search

Description

Get the type of variant given one or more reference alleles and the corresponding variant alleles.

Usage

variantType(ref, alt)

Arguments

ref	the reference alleles
alt	the alternate (variant) alleles

Value

variant type for each ref/alt pair, one of:

1. snp (single nucleotide polymorphism)

2. mnp (multiple nucleotide polymorphism)

3. ins (insertion)

4. del (deletion)

5. mix (some combination of the above)

Examples

ref = c("A", "A",   "AA", "AT", "A",  "AA",  "AA",  "AA",  "ATTA", "AAA",  "A",    "TAAA")
alt = c("C", "C,G", "CT", "A",  "AT", "C",  "CAT", "TAAC", "ATA",  "AATA", "T,AT", "TAA,TAAAA")
print(cbind(ref, alt, variantType(ref, alt)))

chambm/customProDB documentation built on May 31, 2019, 12:08 p.m.