R6 Class for loading and analysing BLAST results in basic Pairwise format

BLAST results are a fundamental unit of basic comparative genomics. This R6 object has been implemented for the systematic exploration of BLAST results within the scope of the Lodestar project.

Super class

floundeR::FloundeR -> Blast

Public fields

blast_file

the file.path to the query BLAST results file

Methods

Public methods

• Blast$new()

• Blast$count()

• Blast$clone()

Inherited methods

• floundeR::FloundeR$bin_data()

• floundeR::FloundeR$num_scale()

• floundeR::FloundeR$nums_scale()

• floundeR::FloundeR$print()

---

Method new()

Creates a new Blast object. This initialisation method performs other sanity checking of the defined file(s) to ensure that it is indeed parseable and creates the required data structures.

Usage

Blast$new(blast_file)

Arguments

blast_file

The source sequencing_summary file.

Returns

A new Blast object.

Examples

blast_results <- flnDr("drosophila_uniref100.blastx.gz")
blast <- Blast$new(blast_file=blast_results)

---

Method count()

Return the number of BLAST results that are contained within the BLAST file provided.

Usage

Blast$count()

---

Method clone()

The objects of this class are cloneable with this method.

Usage

Blast$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

## ------------------------------------------------
## Method `Blast$new`
## ------------------------------------------------

blast_results <- flnDr("drosophila_uniref100.blastx.gz")
blast <- Blast$new(blast_file=blast_results)
#> Error in .check_path("blast_file", blast_file): path [/tmp/Rtmpqr71Kn/temp_libpath14ba6f8cb076/floundeR/extdata/NA] does not exist