get_raw_counts_allele: get_raw_counts_allele

In MitoHEAR: Quantification of Mitochondrial DNA Heteroplasmy

get_raw_counts_allele

Description

It is one the two main function of the MitoHEAR package (together with get_heteroplasmy). The function allows to obtain a matrix of counts (n_row = number of sample, n_col= 4*number of bases) of the four alleles in each base, for every sample. It takes as input a vector of sorted bam files (one bam file for each sample) and a fasta file for the genomic region of interest. It is based on the pileup function of the package Rsamtools.

Usage

get_raw_counts_allele(bam_input, path_fasta, cell_names, cores_number = 1)

Arguments

bam_input	Character vector of sorted bam files (full path). Each sample is defined by one bam file. For each bam file it is needed also the index bam file (.bai) at the same path.
path_fasta	Character string with full path to the fasta file of the genomic region of interest.
cell_names	Character vector of sample names.
cores_number	Number of cores to use.

Value

A list with three elements:

matrix_allele_counts	Matrix of counts (n_row = number of sample, n_col= 4*number of bases) of the four alleles in each base, for every sample. The row names is equal to cell_names.
name_position_allele	Character vector with length equal to n_col of matrix_allele_counts. Each element specifies the coordinate of genomic position for a base and the allele.
name_position	Character vector with length equal to n_col of matrix_allele_counts. Each element specifies the coordinate of genomic position for a base.

Author(s)

Gabriele Lubatti [e-mail]

See Also

https://www.rdocumentation.org/packages/Rsamtools/versions/1.24.0/topics/pileup

MitoHEAR documentation built on March 18, 2022, 6:47 p.m.