sequnce_alignment_threshold: Function for finding threshold of sequence alignment. The...

In LiuzLab/TraceQC: Quality Control of CRISPR Lineage Tracing Seqence Data

Function for finding threshold of sequence alignment. The function randomly permutate certain percentage reference sequence and perform global alignment with the original reference sequence. By use the permutated sequence alignment score, users can filter the TraceQC alignment result.

Description

Function for finding threshold of sequence alignment. The function randomly permutate certain percentage reference sequence and perform global alignment with the original reference sequence. By use the permutated sequence alignment score, users can filter the TraceQC alignment result.

Usage

sequnce_alignment_threshold(
  ref_file,
  match = 2,
  mismatch = -2,
  gapopen = -6,
  gapextension = -0.1,
  permutate_percent = c(0.1, 0.2, 0.3, 0.4, 0.5, 0.6),
  n = 100,
  output_file = "alignment_threshold.txt"
)

Arguments

ref_file	A path of a reference sequence file.
match	The score for a correct basepair matching.
mismatch	The penalty score for a basepair mismatching.
gapopen	The gap opening score for the alignment.
gapextension	The gap extension score for the alignment.
n	number of random permutation used for each percentage
output_file	The output path. An output dataframe will be stored at the path.
corrupted	percentage The number of cores for the parallel processing

Value

It returns a data frame of the alignment result

LiuzLab/TraceQC documentation built on April 19, 2022, 1:29 p.m.