aggregate_NCBI_BLAST_XMLs2DT: Aggregates NCBI BLAST results from multiple XML files into an...

In YoannPa/NCBI.BLAST2DT: Submit DNA sequences to NCBI BLAST and get results in an R data.table.

Aggregates NCBI BLAST results from multiple XML files into an R data.table.

Description

Aggregates NCBI BLAST results from multiple XML files into an R data.table.

Usage

aggregate_NCBI_BLAST_XMLs2DT(dir.to.xmls, seq.names = NULL, ncores = 1)

Arguments

dir.to.xmls	A character specifying a directory to be searched recursively for NCBI BLAST XML results (For more information about XML results from NCBI BLAST see NCBI_BLAST_XML2DT).
seq.names	A character vector to specify sequence names from which you wish to load BLAST results in the R data.table. Useful if your result folder contains results from other BLAST submissions. If NULL, all results in 'dir.to.xmls' will be loaded into the data.table.
ncores	An integer specifying the number of cores or threads to be used for parallel processing.

Value

A data.table aggregating all NCBI BLAST results from all XML files found.

Author(s)

Yoann Pageaud.

References

• The Statistics of Sequence Similarity Scores.

• hoardeR: Collect and Retrieve Annotation Data for Various Genomic Data Using Different Webservices.

• xml2: Parse XML.

Examples

#Aggregate my NCBI BLAST results using 2 cores into an R data.table 
aggregate_NCBI_BLAST_XMLs2DT(dir.to.xmls = "my_dir/with/NCBI_BLAST_results/",
  ncores = 2)

YoannPa/NCBI.BLAST2DT documentation built on Sept. 14, 2024, 2:30 a.m.