makeBaseCalls: Make Basecalls

In sangerseqR: Tools for Sanger Sequencing Data in R

Description

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

Usage

makeBaseCalls(obj, ratio = 0.33)

## S4 method for signature '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.

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.

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.

See Also

chromatogram, setAllelePhase, sangerseq

Examples

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

Example output

Loading required package: Biostrings
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

sangerseqR documentation built on Nov. 8, 2020, 6:52 p.m.