| posSort {HLAtools} | R Documentation |
Numerical Sort of Alignment Positions that Contain Indels
Description
Sorts sequence alignment positions that contain indels in numerical order; e.g., three indels following position X are are identified as X.1, X.2 and X.3.
Positions are validated against a specified locus for a specified alignment type. Positions that do not exist for that locus-alignment combination are not returned.
Usage
posSort(posVec, alignType, locus)
Arguments
posVec |
A character vector of variant positions. |
alignType |
A character string describing the type of alignment the positions are found in. The values 'prot', 'codon', 'nuc' and 'gen' are valid options. Only one 'alignType' value is allowed. |
locus |
A character string describing a locus in the HLAalignments object for the specified alignType. |
Value
A character string of the correctly sorted sequence.
Note
Indel positions must be text-formatted (e.g. "607.12"). C.f., posSort(c(2,4,3,1,5), "nuc","DRB1") vs posSort(c("607.23","607.10","607.3","607.4"),"nuc","DRB1").