Find fragment peaks

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

Usage

find_fragments(
  fragments_trace_list,
  smoothing_window = 21,
  minimum_peak_signal = 20,
  min_bp_size = 100,
  max_bp_size = 1000,
  ...
)

Arguments

fragments_trace_list

A list of fragments_trace objects containing fragment data.

smoothing_window

numeric: signal smoothing window size passed to pracma::savgol()

minimum_peak_signal

numeric: minimum signal of the raw trace. To have no minimum signal set as "-Inf".

min_bp_size

numeric: minimum bp size of peaks to consider

max_bp_size

numeric: maximum bp size of peaks to consider

...

pass additional arguments to pracma::findpeaks(), or change the default arguments we set. minimum_peak_signal above is passed to pracma::findpeaks() as minpeakheight, and peakpat has been set to '[+]{6,}[0]*[-]{6,}' so that peaks with flat tops are still called, see https://stackoverflow.com/questions/47914035/identify-sustained-peaks-using-pracmafindpeaks

Value

a list of fragments_repeats objects.

Details

find_fragments() takes in a list of fragments_trace objects and returns a list of new fragments_repeats objects.

This function is basically a wrapper around pracma::findpeaks. As mentioned above, the default arguments arguments of pracma::findpeaks can be changed by passing them to find_fragments with ... .

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())

find_ladders(fsa_list)
#> 
  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%

fragments_list <- find_fragments(fsa_list,
  min_bp_size = 300
)


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