trace (version 1.0.0)

extract_repeat_correction_summary: Extract repeat correction summary

Description

Extracts a table summarizing the model used to correct repeat length

Usage

extract_repeat_correction_summary(fragments_list)

Value

A data.frame

Arguments

fragments_list

A list of fragments 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)

Examples

fsa_list <- lapply(cell_line_fsa_list, function(x) x$clone())
# import data with read_fsa() to generate an equivalent list to cell_line_fsa_list
test_fragments <- trace(
   fsa_list, 
   grouped = TRUE, 
   metadata_data.frame = metadata, 
   correction = "repeat",
   show_progress_bar = FALSE
)

# finally extract repeat correction summary
extract_repeat_correction_summary(test_fragments)