checkSequenceNames: MitoTrace - an R package for the investigation of...

In lkmklsmn/MitoTrace: A computational framework for investigating mitochondrial heteroplasmies in RNA sequencing data

MitoTrace - an R package for the investigation of mitochondrial heteroplasmies.

Description

The MitoTrace function calculates mitochondrial heteroplasmies in (single-cell) RNA sequencing data based on the reads pileups of the mitochondrial genome.

Usage

MitoTrace(bam_list = bams, ref_fasta = fasta_loc, name = "MT", max_depth = "", 
       min_base_quality = "", min_mapq = "", min_nucleotide_depth = "", min_minor_allele_depth = "")

Arguments

bams_list	Vector of absolute path(s) pointing to BAM alignment file(s).
ref_fasta	Absolute path to the mitochondrial reference genome in FASTA format.
name	Name of mitochondrial genome as specified in the BAM files. Sequence names can be check with the checkSequenceNames() function.
tag_name	The name of the tag corresponding the cellular barcode. Default = "CB". For droplet scRNAseq only.
min_read	The minimum number of read counts to be considered a valid barcode (cell) in the analysis. Default = 1000. For droplet scRNAseq technologies only.
max_depth	The maximum depth of reads considered at any position.
min_base_quality	The minimum read base quality below which the base is ignored when summarizing pileup information.
min_mapq	The minimum mapping quality below which the entire reads is ignored.
min_nucleotide_depth	integer(1); minimum count of each nucleotide at a given position required for said nucleotide to appear in the result.
min_minor_allele_depth	integer(1); minimum count of all nucleotides other than the major allele at agiven position.

Details

result <- MitoTrace(bam_list = bams, ref_fasta = fasta_loc, chr_name = "MT", max_depth = "1e6", min_base_quality=25, min_mapq=30, min_nucleotide_depth=0, min_minor_allele_depth=0)

See packageDescription("MitoTrace") for more details.

Value

Read counts matrix and coverage matrix.

Note

This package could not only apply for the analysis of single-cell data but also for bulk seuqencing data.

Author(s)

Mingqiang WANG <[e-mail]>, Simon Lukas <[e-mail]>

References

The current source code of MitoTrace is from https://github.com/lkmklsmn/MitoTrace.

lkmklsmn/MitoTrace documentation built on June 29, 2023, 5:55 a.m.