sangerseqR (version 1.8.2)

makeBaseCalls: Make Basecalls

Description

Updates a sangerseq class object to contain primary and secondary peak calls.

Usage

makeBaseCalls(obj, ratio = 0.33)
## S3 method for class 'sangerseq':
makeBaseCalls(obj, ratio = 0.33)

Arguments

obj

sangerseq class object

ratio

cutoff ratio for separating signal and noise. Ratio is relative to maximum peak in basecall window.

Value

• sangerseq s4 object with new basecalls in the primarySeq and secondarySeq fields. Matrix values are also updated to reflect newly called base positions and amplitudes of all peaks within window.

Details

Scf files do not contain secondary basecalls and ABIF files sometimes (but not always) contain secondary peak calls that show the secondary peak even if clearly a negative peak. This is problematic in sequence reads where heterozygous sequence data is contained in the chromatogram data. makeBaseCalls identifies basecall windows containing more than one peak using the provided cutoff ratio and then makes heterozygous calls for those windows. The primarySeq will always contain the base corresponding to the maximum peak amplitude within the window. The secondaryPeak will have the same base if the peak was classified as a homozygous peak, the base corresponding to the second tallest peak if two peaks were above the cutoff, or an ambiguous base if more than two peaks were identified in the window that are higher than the cutoff ratio.

See Also

chromatogram, setAllelePhase, sangerseq

Examples

hetsangerseq <- readsangerseq(system.file("extdata",
                                          "heterozygous.ab1",
                                          package = "sangerseqR"))
hetcalls <- makeBaseCalls(hetsangerseq, ratio = 0.33)