Generate Mismatches for a primer sequence

Create a vector of sequences with all possible SNP mutations (single base pair mismatches) given a string sequence

mismatchGenerator(seq, saveList = FALSE)

Arguments

seq

Primer sequence to generate mismatches for

saveList

Boolean, if this is set to true the list will be saved in cache$mismatchDict for later reference. Note: If there are many primers, or they are particularly long, then this can cause memory errors as lists can be long especially on second generation (2 mismatch lists)

Value

vector of all possible SNP mutations

Examples

mismatchGenerator("AATTTGTGTCAA")
#> [[1]]
#> [1] "TATTTGTGTCAA"
#> 
#> [[2]]
#> [1] "CATTTGTGTCAA"
#> 
#> [[3]]
#> [1] "GATTTGTGTCAA"
#> 
#> [[4]]
#> [1] "ATTTTGTGTCAA"
#> 
#> [[5]]
#> [1] "ACTTTGTGTCAA"
#> 
#> [[6]]
#> [1] "AGTTTGTGTCAA"
#> 
#> [[7]]
#> [1] "AAATTGTGTCAA"
#> 
#> [[8]]
#> [1] "AACTTGTGTCAA"
#> 
#> [[9]]
#> [1] "AAGTTGTGTCAA"
#> 
#> [[10]]
#> [1] "AATATGTGTCAA"
#> 
#> [[11]]
#> [1] "AATCTGTGTCAA"
#> 
#> [[12]]
#> [1] "AATGTGTGTCAA"
#> 
#> [[13]]
#> [1] "AATTAGTGTCAA"
#> 
#> [[14]]
#> [1] "AATTCGTGTCAA"
#> 
#> [[15]]
#> [1] "AATTGGTGTCAA"
#> 
#> [[16]]
#> [1] "AATTTATGTCAA"
#> 
#> [[17]]
#> [1] "AATTTTTGTCAA"
#> 
#> [[18]]
#> [1] "AATTTCTGTCAA"
#> 
#> [[19]]
#> [1] "AATTTGAGTCAA"
#> 
#> [[20]]
#> [1] "AATTTGCGTCAA"
#> 
#> [[21]]
#> [1] "AATTTGGGTCAA"
#> 
#> [[22]]
#> [1] "AATTTGTATCAA"
#> 
#> [[23]]
#> [1] "AATTTGTTTCAA"
#> 
#> [[24]]
#> [1] "AATTTGTCTCAA"
#> 
#> [[25]]
#> [1] "AATTTGTGACAA"
#> 
#> [[26]]
#> [1] "AATTTGTGCCAA"
#> 
#> [[27]]
#> [1] "AATTTGTGGCAA"
#> 
#> [[28]]
#> [1] "AATTTGTGTAAA"
#> 
#> [[29]]
#> [1] "AATTTGTGTTAA"
#> 
#> [[30]]
#> [1] "AATTTGTGTGAA"
#> 
#> [[31]]
#> [1] "AATTTGTGTCTA"
#> 
#> [[32]]
#> [1] "AATTTGTGTCCA"
#> 
#> [[33]]
#> [1] "AATTTGTGTCGA"
#> 
#> [[34]]
#> [1] "AATTTGTGTCAT"
#> 
#> [[35]]
#> [1] "AATTTGTGTCAC"
#> 
#> [[36]]
#> [1] "AATTTGTGTCAG"
#>