Hsp-class: Class '"Hsp"'

In gschofl/blastr: A wrapper for NCBI Blast

Description

An S4 class that serves as a container for information parsed from an NCBI BLAST XML high-scoring pair (hsp) element.

Slots

hsp_num

The number of the hsp; "integer".

score

The BLAST score of the hsp; "numeric".

bit_score

The bit score of the hsp; "numeric".

evalue

The expect value; "numeric".

identity

Number of identities; "integer".

positive

Number of positives; "integer".

gaps

Number of gaps; "integer".

query_from

Start residue for query sequence; "integer".

query_to

End residue for query sequence; "integer".

hit_from

Start residue for hit sequence; "integer".

hit_to

End residue for hit sequence; "integer".

query_frame

"integer".

hit_frame

"integer".

qseq

Query sequence; "XString".

hseq

Hit sequence; "XString".

match

Match sequence/midline; "XString".

query_env

Shared container for query_id, query_def, query_len, and hit_len; "environment".

See Also

"BlastReport"

Examples

showClass("Hsp")

gschofl/blastr documentation built on May 17, 2019, 8:52 a.m.