samePeaks: samePeaks

In LazyMLVA: LazyMLVA

Description

The function determines whether peaks in two electropherogram files (ABIF files) represent the same size standard or not. ABIF files have to be imported using the function seqinr::read.abif.

Usage

samePeaks(e1, 
          e2, 
          ch = 5, 
          npks = 15, 
          e1_tmin = 2.3, 
          e1_thres = 0.5, 
          e2_tmin = e1_tmin, 
          e2_thres = e1_thres, 
          dist_thres = 0.01, 
          s_warn = -1)

Arguments

e1	electropherogram 1 imported with seqinr::read.abif
e2	electropherogram 1 imported with seqinr::read.abif
ch	channel number; see (see function seqinr::peakabif)
npks	expected number of peaks
e1_tmin	starting time for the time axis for e1 (see function seqinr::peakabif)
e1_thres	threshold, above which peaks are looked for in e1 (see function seqinr::peakabif)
e2_tmin	starting time for the time axis for e2 (see function seqinr::peakabif)
e2_thres	threshold, above which peaks are looked for in e2 (see function seqinr::peakabif)
dist_thres	euclidian distance, below which function returns TRUE
s_warn	sets the handling of warning messages; see options()

Value

logical() value TRUE or FALSE

Author(s)

Johannes Elias

References

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

See Also

seqinr::peakabif

Examples

# the following returns TRUE 
samePeaks(r_abif,r_abif)

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