Description Usage Format Value Constructor Methods Examples
This class will allow to load, convert and normalize alignments and regions files/data.
1 |
A BAM manager
Bam_Handler$new
returns a Bam_Handler
object which contains
coverage related information for every BAM files.
bh <- Bam_Handler$new(bam_files, cores = SerialParam())
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 or file.bai in the same
directory.
The number of cores available to parallelize the analysis.
Either a positive integer or a BiocParallelParam
.
Default: SerialParam()
.
If TRUE
, metagene will deal with paired-end
data. If FALSE
, single-end data are expected
Bam_Handler$new
returns a Bam_Handler
object that contains
and manages BAM files. Coverage related information as alignment count can
be obtain by using this object.
bh$get_aligned_count(bam_file)
The name of the BAM file.
bg$get_bam_name(bam_file)
The name of the BAM file.
bh$get_rpm_coefficient(bam_file)
The name of the BAM file.
bh$index_bam_files(bam_files)
A vector
of BAM filenames.
bh$get_bam_files()
bh$get_coverage(bam_file, regions)
force_seqlevels = FALSE)
The name of the BAM file.
A not empty GRanges
object.
If TRUE
, Remove regions that are not found
in bam file header. Default: FALSE
. TRUE and FALSE
respectively correspond to pruning.mode = "coarse"
and "error" in ?seqinfo.
bh$get_normalized_coverage(bam_file, regions)
force_seqlevels = FALSE)
The name of the BAM file.
A not empty GRanges
object.
If TRUE
, Remove regions that are not found
in bam file header. Default: FALSE
. TRUE and FALSE
respectively correspond to pruning.mode = "coarse"
and "error" in ?seqinfo.
bh$get_noise_ratio(chip_bam_file, input_bam_file)
The path to the chip bam file.
The path to the input (control) bam file.
1 2 3 | bam_file <- get_demo_bam_files()[1]
bh <- metagene:::Bam_Handler$new(bam_files = bam_file)
bh$get_aligned_count(bam_file)
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