read_blast_xml: Parse BLAST XML output
In robbueck/wisard: Perform wighted interval scheduling on a Genomic Ranges object

Description Usage Arguments Details Value

View source: R/read_blast.R

Parses a BLAST xml-file to a GRangesList or data.frame object.

1	read_blast_xml(x, grange_output = T, keep_sequences = F)

`x`	A xml file created with NCBI-BLAST option -outfmt 5 or AB-BLAST option -mformat=7.
`grange_output`	If set TRUE, output is a GRangesList object, otherwise a data.frame object.
`keep_sequences`	If FALSE, sequence and alignment columns are discarded.

This function parses BLAST-xml output files using xmlParse. Setting keep_sequences FALSE will discard all sequence and alignment columns to save memory.

A list with two elements accessible via:
$metadata: BLAST-metadata such as run parameters, sequence information and statistics.
$alignments: Information about the alignments.
If grange_output is set FALSE, output is a data.frame object, else a GRangesList object with start, end, strand, sequence name and length taken from the subject. Information about the query is presered in the metadata columns.

robbueck/wisard documentation built on Jan. 25, 2022, 12:35 a.m.