R: get_raw_counts

get_raw_counts_allele {MitoHEAR}

R Documentation

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)