strvalidator (version 1.3.0)

combineBinsAndPanels: combine bins and panels files.

Description

combineBinsAndPanels combines useful information into one dataset.

Usage

combineBinsAndPanels(bin, panel)

Arguments

bin

data frame created from the 'bins' file.

panel

data frame created from the 'panels' file.

Value

• data frame containing columns 'Panel', 'Marker', 'Allele', 'Size', 'Size.Min', 'Size.Max', 'Virtual', 'Color', 'Repeat', 'Marker.Min', 'Marker.Max', 'Offset', 'Short.Name', 'Full.Name'

Details

Combines information from two sources ('Bins' and 'Panels' file) to create a dataset containing information about panel name, marker name, alleles in the allelic ladder, their size and size range, a flag indicating virtual alleles, fluorophore color, repeat size, marker range. The short name, full name, and gender marker flag is populated through the makeKit_gui user interface. In addition the function calculates an estimated offset for each marker, which can be used for creating epg-like plots. Note: offset is estimated by taking the smallest physical ladder fragment e.g. 98.28 for D3 in ESX17. Round this to an integer (98) and finally subtract the number of base pair for that repeat i.e. 4*9=36, which gives an offset of 98-36 = 62 bp. Microvariants are handled by taking the decimal part multiplied with 10 and adding this to the number of base pair e.g. 9.3 = 4*9 + 0.3*10 = 39 bp.