fun_analysis: Analyzing function.

In MicroSEC: Sequence Error Filter for Formalin-Fixed and Paraffin-Embedded Samples

Analyzing function.

Description

This function analyzes the filtering results.

Usage

fun_analysis(
  msec,
  mut_depth,
  short_homology_search_length,
  min_homology_search,
  threshold_p,
  threshold_hairpin_ratio,
  threshold_short_length,
  threshold_distant_homology,
  threshold_soft_clip_ratio,
  threshold_low_quality_rate,
  homopolymer_length
)

Arguments

msec	Mutation filtering information.
mut_depth	Mutation coverage data.
short_homology_search_length	Small sequence for homology search.
min_homology_search	The sequence length for homology search.
threshold_p	The largest p value of significant errors.
threshold_hairpin_ratio	The smallest hairpin read ratio.
threshold_short_length	Reads shorter than that are analyzed.
threshold_distant_homology	The smallest rate of reads from other regions.
threshold_soft_clip_ratio	The rate of soft-clipped reads.
threshold_low_quality_rate	The smallest rate of low quality bases.
homopolymer_length	The smallest length of homopolymers.

Value

msec

Examples

data(msec_summarized)
data(mut_depth_checked)
fun_analysis(msec = msec_summarized,
             mut_depth = mut_depth_checked,
             short_homology_search_length = 4,
             min_homology_search = 40,
             threshold_p = 10 ^ (-6),
             threshold_hairpin_ratio = 0.50,
             threshold_short_length = 0.75,
             threshold_distant_homology = 0.15,
             threshold_soft_clip_ratio = 0.50,
             threshold_low_quality_rate = 0.1,
             homopolymer_length = 15
)

MicroSEC documentation built on Sept. 11, 2024, 6:06 p.m.