Group trimmed sequences into aligning groups

indexGroups(blast, fasta, mode = "any", aln.size)

Arguments

blast

BLAST alignment table to process.

fasta

Epitope sequence AAStringset object to process.

mode

Grouping method. "any" creates a smaller number of groups, with individual groups tending to have more members, such that in each group, each member must align with at least 1 "any" of the other members. "all" creates a larger number of groups, with individual groups tending to have fewer members, wuch taht in each group, each member must align with "all" other members.

aln.size

Minimum length of alignment to consider from BLASTp alignments of 'data'.