samePeaks: samePeaks

Description Usage Arguments Value Author(s) References See Also Examples

View source: R/LazyMLVA.R

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

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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

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# the following returns TRUE 
samePeaks(r_abif,r_abif)

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