Bam_Handler: A class to manage BAM files.

Description

This class will allow to load, convert and normalize alignments and regions files/data.

Usage

Bam_Handler

Arguments

Value

Bam_Handler$new returns a Bam_Handler object which contains coverage related information for every BAM files.

Format

A BAM manager

Constructor

: bh <- Bam_Handler$new(bam_files, cores = SerialParam())
bam_files: A vector of BAM filenames. The BAM files must be indexed. i.e.: if a file is named file.bam, there must be a file named file.bam.bai in the same directory.
cores: The number of cores available to parallelize the analysis. Either a positive integer or a BiocParallelParam. Default: SerialParam().

Bam_Handler$new returns a Bam_Handler object that contains and manages BAM files. Coverage related information as alignment count can be obtain by using this object.

Methods

: bh$get_aligned_count(bam_file)
bam_file: The name of the BAM file.

: bg$get_bam_name(bam_file)
bam_file: The name of the BAM file.

: bh$get_rpm_coefficient(bam_file)
bam_file: The name of the BAM file.

: bh$index_bam_files(bam_files)
bam_files: A vector of BAM filenames.

: bh$get_bam_files()

: bh$get_coverage(bam_file, regions) force_seqlevels = FALSE)
bam_file: The name of the BAM file.
regions: A not empty GRanges object.
force_seqlevels: If TRUE, Remove regions that are not found in bam file header. Default: FALSE.

: bh$get_normalized_coverage(bam_file, regions) force_seqlevels = FALSE)
bam_file: The name of the BAM file.
regions: A not empty GRanges object.
force_seqlevels: If TRUE, Remove regions that are not found in bam file header. Default: FALSE.

: bh$get_noise_ratio(chip_bam_file, input_bam_file)
chip_bam_file: The path to the chip bam file.
input_bam_file: The path to the input (control) bam file.

Examples

Run this code

bam_file <- get_demo_bam_files()[1]
bh <- metagene:::Bam_Handler$new(bam_files = bam_file)
bh$get_aligned_count(bam_file)

Run the code above in your browser using DataLab