| combineBinsAndPanels {strvalidator} | R Documentation |
Combine Bins And Panels Files.
Description
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. |
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 sex 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.
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'