LazyMLVA-package: LazyMLVA

In LazyMLVA: LazyMLVA

Description

The package automates assignment of MLVA types. MLVA stands for 'Multiple-Locus- VNTR-Analysis', which is a typing approach for bacterial pathogens. It extracts the size standard from ABIF electropherogram files and automatically looks for products of unknown sizes in the specified channels. Further to estimating the sizes of found products, it converts the sizes to repeat lengths according to data specified in a 'lazy map'. The package depends on seqinr.

Function sizeCaller extracts the size ladder from the electropherogram and handles conversion of time to basepairs (see ?sizeCaller for details).

Function vntrLoci analyzes files within a specified directory according to details given in a 'lazy map' (see ?vntrLoci and ?lazy.map for details regarding the function and the 'lazy map', respectively).

Function plotabif2 visualizes the contents of an ABIF file. See ?plotabif2 for details.

Details

Package:	LazyMLVA
Type:	Package
Version:	0.0-6
Date:	2010-01-25
License:	GPL
LazyLoad:	yes

Author(s)

Johannes Elias

Maintainer: Johannes Elias <[e-mail]>

References

citation(package="seqinr")

Applied Biosystems. (2009) Applied Biosystems Genetic Analysis Data File Format [Online]. Available from: http://www.appliedbiosystems.com/support/software_community/ABIF_File_Format.pdf (Accessed: 14 January 2010).

See Also

seqinr::peakabif, seqinr::read.abif

Examples

# show a nice plot of the time->bp conversion function
searchStandardPeaks(r_abif,plotit=TRUE)

# plot channels of reference abif file r_abif
plotabif2(r_abif)

# returns the sizes of peaks in the standard ABIF file
sizeCaller(r_abif)

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

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