sizeCaller: sizeCaller

In LazyMLVA: LazyMLVA

Description

The function extracts positions of standard peaks from an ABIF file and calculates the sizes of products in specified channels.

Usage

sizeCaller(x_abifile, 
            rsizes = r_sizes, 
            ranges = matrix(rep(c(2.3, 8), sum(npeaks.per.channel)), nrow = sum(npeaks.per.channel), byrow = TRUE), 
            ranges.bp, 
            thres_start = 2, 
            channels = 1:4, 
            npeaks.per.channel = rep(1, length(channels)), 
            locus.names = paste(rep("V", length(channels)), 1:sum(npeaks.per.channel), sep = ""), 
            strain.name = deparse(substitute(x_abifile)), 
            ...)

Arguments

x_abifile	list generated by seqinr::read.abif representing the ABIF file
rsizes	sizes of reference peaks in basepairs. peaks not to be counted are given as NA.
ranges	matrix of time ranges across which peaks are looked for in channels specified in channels
ranges.bp	matrix of basepair ranges across which peaks are looked for in channels specified in channels. If given, this matrix overrides matrix ranges.
thres_start	threshhold, below which peaks are looked for (see function seqinr::peakabif)
channels	channel numbers containing products of unknown sizes
npeaks.per.channel	array containing number of peaks per channel (defaults to one peak per channel)
locus.names	array of locus names
strain.name	name of strain to be analyzed
...	arguments passed on to searchStandardPeaks(...)

Value

matrix returning the peak sizes in basepairs of each locus

Warning

Warnings are issued if sizes in one or several loci cannot be calculated or if searchStandardPeaks is unable to extract the standard ladder from x_abifile.

Author(s)

Johannes Elias

References

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

See Also

searchStandardPeaks, r_sizes

Examples

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

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