BlastTable-class: Class '"BlastTable"'

In gschofl/blastr: A wrapper for NCBI Blast

Description

An S4 class that serves as a container for data parsed from NCBI BLAST tabular output.

Usage

## S4 method for signature 'BlastTable'
x$name

## S4 method for signature 'BlastTable'
x[i, j, ..., drop = TRUE]

## S4 method for signature 'BlastTable'
x[[i]]

## S4 method for signature 'BlastTable'
names(x)

Methods (by generic)

• $: Return a column from a BLAST hit table.

• [: Return selected elements from a BLAST hit table as a data.frame.

• [[: Return selected columns from a BLAST hit table.

• names: Get the column names from a BLAST hit table.

Slots

program

<character>; The BLAST flavour that generated the data.

query

<character>; Query definition.

reference

<character>; Reference for BLAST.

database

<character>; Name of the database.

bit_score

<numeric>; The bit score of the hsp.

evalue

<numeric>; The expect value.

mlog.evalue

<numeric>;

accession

<character>; Accession number.

geneid

<character>; NCBI GI number.

table

<data.frame>; Hit table.

See Also

The constructor blastTable; the BLAST classes BlastReport and BlastReportDB

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