BlastParameters-class: Class '"BlastParameters"'

In gschofl/blastr: A wrapper for NCBI Blast

Description

An S4 class that that serves as the container for blast parameters and statistics.

Slots

program

character vector; the BLAST flavour that generated the data.

matrix

character vector; name of the matrix (NA for nucleotide blast).

expect

numeric vector; cutoff value.

penalties

numeric vector; open and extend penalties.

sc_match

integer vector; match score for nucleotide-nucleotide comparison.

sc_mismatch

integer vector; mismatch penalty for nucleotide- nucleotide comparison.

filter

character vector; filter string.

num_sequences

character vector; number of sequences in the database.

num_letters

character vector; number of letters in the database.

hsp_length

numeric vector; effective HSP length.

effective_space

numeric vector; effective search space.

ka_params

numeric vector; kappa, lambda, entropy.

See Also

BlastReport, BlastHeader

Examples

showClass("BlastParameters")

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