create_TraceQC_object: Creating an input object for TraceQC with an alignment...

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

Creating an input object for TraceQC with an alignment result.

Description

Creating an input object for TraceQC with an alignment result.

Usage

create_TraceQC_object(
  aligned_reads_file,
  ref_file,
  fastqc_file,
  use_CPM = TRUE,
  alignment_score_cutoff = 0,
  abundance_cutoff = 0,
  ncores = 1
)

Arguments

aligned_reads_file	A path to store alignment output file.
ref_file	A path of a reference sequence file.
fastqc_file	A path of a FASTQC file.
use_CPM	Use count per million
alignment_score_cutoff	Minimum cutoff for alignment score
abundance_cutoff	Minimum cutoff for read count. This parameter are used with use_CPM.
ncores	The number of cores for the parallel processing.

Value

A list with those four elements.

• ‘aligned_reads’: an data frame that contains alignment information.

• ‘refseq’: The reference sequence.

• ‘regions’: Detailed information about the reference sequence.

• ‘qc’: A list of tibbles containing the QC data.

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