get the high score region(HSP) from the given alignment result

HSP {bioseq.blast}

R Documentation

get the high score region(HSP) from the given alignment result

Description

Usage

HSP(align, cutoff, minW,
    as.dataframe = TRUE);

Arguments

align

a SmithWaterman local alignment result object, which is the output of the align.smith_waterman api. [as SmithWaterman]

cutoff

the similarity score cutoff threshold value in [0,1] for filter the candidate HSP regions. [as double]

minW

the minimum region size in chars of the candidate HSP regions, the HSP region that its size is smaller than this threshold value will be ignored. [as integer]

as.dataframe

cast the HSP result as a data frame object? if this parameter is FALSE, then a vector of the HSP object will be returned instead. [as boolean]

Authors

seqtoolkit

Value

a data frame object of the HSP alignment details(the columns are: query, subject, query_length, subject_length, length_query, length_hit, hsp_query, hsp_subject, score and coverage) when the as_dataframe parameter is TRUE, or a vector of the HSP object when this parameter is FALSE.

clr value class

[Package bioseq.blast version 1.0.0.0 Index]