searchStandardPeaks: searchStandardPeaks

In LazyMLVA: LazyMLVA

Description

The function looks for the standard size ladder in an electropherogram (ABIF) file. ABIF files have to be imported using seqinr::read.abif(). If successful, the function returns the peak positions the size standard.

Usage

searchStandardPeaks(x_abifile, 
                    refchannel = 5, 
                    reference = r_npk, 
                    npks = 15, 
                    rsizes = r_sizes, 
                    x_tmin = 2, 
                    x_tmax = 3, 
                    x_thres = 0.5, 
                    x_step = 0.1, 
                    dist_thres = 0.01, 
                    plotit = FALSE, 
                    ...)

Arguments

x_abifile	list generated by seqinr::read.abif representing the ABIF file
refchannel	channel number of the size ladder. See seqinr::peakabif.
reference	contains normalized peak positions. Peak positions can be extracted from an ABIF file with seqinr::peakabif. Normalization is achieved with normPeaks.
npks	number of expected peaks
rsizes	sizes of reference peaks in basepairs; peaks not to be counted are given as NA.
x_tmin	scaled (1:1000) starting time for the time axis for x_abifile (see function seqinr::peakabif)
x_tmax	scaled (1:1000) ending time for the time axis for x_abifile (see function seqinr::peakabif)
x_thres	threshold, above which peaks are looked for in x_abifile (see function seqinr::peakabif)
x_step	step, by which x_thres is decreased and x_tmin increased until standard peaks are retrieved
dist_thres	euclidian distance of peak vectors, below which identity of references in x_abifile and reference is assumed
plotit	logical value stating whether a time->bp plot should be shown
...	arguments passed to plot

Value

numeric vector containing the positions of the standard peaks

Warning

A warning is issued if standard peaks cannot be retrieved.

Author(s)

Johannes Elias

References

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

See Also

sizeCaller

Examples

# returns positions of reference peaks in reference file
searchStandardPeaks(r_abif)

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

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