hoardeR (version 0.9.2)

importXML: Import an XML File produced by the blastSeq function

Description

This function imports an xml file produced from blastSeq.

Usage

importXML(folder, seqNames=NULL, which=NULL, idTH = 0.8, verbose=TRUE)

Arguments

folder

Folder where the xml files are stored.

seqNames

Sequence names.

which

Which of the provided sequence names should be imported.

idTH

Identity threshold, see details.

verbose

Logical, function give status messages.

Value

A data frame containing the results.

Details

This function imports xml files produced from the blastSeq function. The idTh options sets the limit, what the minimum id threshold is until a hit will be taken into the result data frame.

If seqNames is NULL (default) and codewhich is NULL (default) all sequences are imported. The list can be limited, either by specifying the sequence name (the file name of it), or its position in the order list of names, using which.