vntrLoci: vntrLoci

In LazyMLVA: LazyMLVA

Description

This function automates the analysis of ABIF files within a directory according to specifications in a 'lazy map'.

Usage

vntrLoci(p, 
        lz.map = lazy.map, 
        file.ending = ".fsa", 
        size.only = FALSE, 
        filename.sep = "_", 
        wide.table = TRUE,
        ...)

Arguments

p	path to directory containing abif files to be analyzed
lz.map	a 'lazy map' is a table listing all loci that are looked for, their basepair ranges, corresponding repeat numbers, etc.
file.ending	file ending of ABIF files
size.only	if TRUE, only sizes in basepairs are given
filename.sep	ABIF filenames are assumed to be of the form NAME + filename.sep + SERIES + file.ending; e.g. 1087_S1.fsa specifies series 'S1' of strain '1087'
wide.table	logical variable stating whether conversion to a nice wide table should be attempted (this only works if the same strains have been specified in each series)
...	arguments passed to sizeCaller(...)

Value

a list of matrices (one matrix per series) containing the repeat numbers of each locus and strain

Author(s)

Johannes Elias

References

package seqinr by Charif, D. and Lobry, J.R. (2007)

Examples

# process ABIF files in directory 'abif'
vntrLoci(system.file("abif",package="LazyMLVA"))

# show sizes only
vntrLoci(system.file("abif",package="LazyMLVA"),size.only=TRUE)

LazyMLVA documentation built on May 2, 2019, 5:33 p.m.