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Find fragment peaks

find_fragments.Rd

Find fragment peaks in continuous trace data and convert to fragments class.

Usage

find_fragments(fragments_list, config, ...)

Arguments

fragments_list

A list of fragments objects containing fragment data.

config

A trace_config object generated using load_config().

...

additional parameters from any of the functions in the pipeline detailed below may be passed to this function. This overwrites values in the config. These parameters include:

  • smoothing_window numeric, signal smoothing window size passed to pracma::savgol(). Default: 21.

  • minimum_peak_signal numeric, minimum signal of the raw trace. To have no minimum signal set as "-Inf". Default: 20.

  • min_bp_size numeric, minimum bp size of peaks to consider. Default: 100.

  • max_bp_size numeric, maximum bp size of peaks to consider. Default: 1000.

  • peak_scan_ramp Single numeric value to indicate how many scans (increasing in signal) should be either side of the peak maxima. Default: 5.

Value

a list of fragments objects.

Details

This takes in a list of fragments objects and returns a list of new fragments objects.

This function is basically a wrapper around pracma::findpeaks(). If your amplicon is large, there may be fewer scans that make up individual peak. So for example you may want to set peak_scan_ramp as a smaller value.

If too many and inappropriate peaks are being called, this may also be solved with the different repeat calling algorithms in call_repeats().

Examples

fsa_list <- lapply(cell_line_fsa_list[1], function(x) x$clone())
config <- load_config()

trace:::find_ladders(fsa_list, config)
#> 
  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%

trace:::find_fragments(fsa_list,
  config,
  min_bp_size = 300
)
#> 
  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%


# Manually inspect the ladders
plot_traces(fsa_list,
  show_peaks = TRUE, n_facet_col = 1,
  xlim = c(400, 550), ylim = c(0, 1200)
)