extract_repeat_correction_summary: Extract repeat correction summary

In trace: Tandem Repeat Analysis by Capillary Electrophoresis

Extract repeat correction summary

Description

Extracts a table summarizing the model used to correct repeat length

Usage

extract_repeat_correction_summary(fragments_list)

Arguments

fragments_list

A list of fragments_repeats class objects obtained from the call_repeats() function when the correction = "repeat" parameter is used.

Details

For each of the samples used for repeat correction, this table pulls out the modal repeat length called by the model (allele_repeat), how far that sample is on average from the linear model in repeat units by finding the average residuals (avg_residual), and the absolute value of the avg_residual (abs_avg_residual)

Value

A data.frame

Examples

fsa_list <- lapply(cell_line_fsa_list[16:19], function(x) x$clone())

find_ladders(fsa_list, show_progress_bar = FALSE)

fragments_list <- find_fragments(fsa_list, min_bp_size = 300)

test_alleles <- find_alleles(
  fragments_list 
)

add_metadata(
  fragments_list,
  metadata
)


call_repeats(
  fragments_list = fragments_list,
  correction = "repeat"
)

# finally extract repeat correction summary
extract_repeat_correction_summary(fragments_list)

trace documentation built on April 4, 2025, 1:50 a.m.