readBlast: Convert NCBI BLAST+ Files to Dataframe

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/readBlast.R

Description

Reads .blast6out files (NCBI Blast Format) generated by the VSEARCH clustering and alignment algorithms.

Usage

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readBlast(
  file,
  minE = 1,
  length = 0,
  identity = 0,
  removeExactMatches = FALSE,
  scope = NULL,
  packMatches = NULL
)

Arguments

file

The file path of the blast file.

minE

Blast results with e values greater than the specified cutoff will be ignored.

length

Blast results alignment lengths lower below this value will be ignored

identity

Blast results with target sequence identities below this value will be ignored.

removeExactMatches

If true, matches with 100 be ignored to prevent self-hits.

scope

If specified, blast results below the specified value will be ignored. Note that the dataframe of transposon matches must also be supplied to calculate scope. Scope is the proportion of the transposon's internal sequence occupied by the BLAST hit.

packMatches

taframe containing genomic ranges and names referring to sequences to be extracted. Can be obtained from packSearch or generated from a GRanges object, after conversion to a dataframe. Must contain the following features:

  • start - the predicted element's start base sequence position.

  • end - the predicted element's end base sequence position.

  • seqnames - character string referring to the sequence name in Genome to which start and end refer to.

Details

blast6out file is tab-separated text file compatible with NCBI BLAST m8 and NCBI BLAST+ outfmt 6 formats. One cluster/alignment can be found for each line.

Value

A dataframe containing the converted .blast6out file. The file contains the following features:

Author(s)

Jack Gisby

References

For further information, see the NCBI BLAST+ application documentation and help pages (https://www.ncbi.nlm.nih.gov/pubmed/20003500?dopt=Citation). VSEARCH may be downloaded from https://github.com/torognes/vsearch; see https://www.ncbi.nlm.nih.gov/pubmed/27781170 for further information.

See Also

codeblastAnalysis, codeblastAnnotate, codepackAlign, codereadUc, codepackClust

Examples

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readBlast(system.file(
    "extdata", 
    "packMatches.blast6out", 
    package = "packFinder"
))

packFinder documentation built on Nov. 8, 2020, 5:24 p.m.