trace (version 1.0.0)

genemapper_table_to_fragments: Convert Genemapper Peak Table to fragments class

Description

This function converts a genemapper peak table data frame into a list of fragments objects.

Usage

genemapper_table_to_fragments(
  df,
  dye_channel,
  min_size_bp = 200,
  max_size_bp = 1000
)

Value

A list of fragments objects.

Arguments

df

A data frame from genemapper containing the peak data.

dye_channel

A character string indicating the Genemapper channel to extract data from. This is used to filter 'Dye.Sample.Peak' for the channel containing the data. For example, 6-FAM is often "B" while ladder is "O".

min_size_bp

Numeric value indicating the minimum size of the peak table to import.

max_size_bp

Numeric value indicating the maximum size of the peak table to import.

Details

This function takes a peak table data frame (eg. Genemapper 5 output) and converts it into a list of fragment objects. It uses the "Sample.File.Name" as the unique id, so make sure that each file as a unique name. Column names should contain: "Dye.Sample.Peak", "Sample.File.Name", "Allele", "Size", "Height".

See Also

repeat_table_to_fragments(), size_table_to_fragments(), read_fsa()

Examples

gm_raw <- trace::example_data

test_fragments <- genemapper_table_to_fragments(
  gm_raw,
  dye_channel = "B",
  min_size_bp = 400
)