indexGroups: Group trimmed sequences into aligning groups

In brandonsie/epitopefindr: Minimal Overlaps from BLAST Alignments

Group trimmed sequences into aligning groups

Description

Group trimmed sequences into aligning groups

Usage

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'.

brandonsie/epitopefindr documentation built on May 4, 2024, 10:27 a.m.