calculatePullup: Calculate Pull-up

Description

calculatePullup calculates possible pull-up peaks.

Usage

calculatePullup(data, ref, pullup.range = 6, block.range = 12,
  ol.rm = FALSE, ignore.case = TRUE, word = FALSE, discard = FALSE,
  debug = FALSE)

Arguments

data

a data frame containing at least 'Sample.Name', 'Marker', 'Height', 'Allele', 'Dye', 'Data.Point' and 'Size'.

ref

a data frame containing at least 'Sample.Name', 'Marker', 'Allele'.

pullup.range

numeric to set the analysis window to look for pull-up peaks (known allele data point +- pullup.range/2)

block.range

numeric to set blocking range to check for known allele overlap (known allele data point +- block.range/2).

ol.rm

logical TRUE if off-ladder peaks should be excluded from analysis. Default is FALSE to include off-ladder peaks.

ignore.case

logical indicating if sample matching should ignore case.

word

logical indicating if word boundaries should be added before sample matching.

discard

logical TRUE if known alleles with no detected pull-up should be discarded from the result. Default is FALSE to include alleles not causing pull-up.

debug

logical indicating printing debug information.

Value

data.frame with with columns 'Sample.Name', 'Marker', 'Dye', 'Allele', 'Height', 'Size', 'Data.Point', 'P.Marker', 'P.Dye', 'P.Allele', 'P.Height', 'P.Size', 'P.Data.Point', 'Delta', 'Ratio'.

Details

Calculates possible pull-up (aka. bleed-through) peaks in a dataset. Known alleles are identified and the analysis window range is marked. If the blocking range of known alleles overlap, they are excluded from the analysis. Pull-up peaks within the data point analysis window, around known alleles, are identified, the data point difference, and the ratio is calculated. Off-ladder ('OL') alleles are included by default but can be excluded. All known peaks included in the analysis are by default written to the result even if they did not cause any pull-up. These rows can be discarded from the result.