rawCounts: rawCounts
In BenjaminAdelaide/msgbsR: msgbsR: methylation sensitive genotyping by sequencing (MS-GBS) R functions
Description
Usage
Arguments
Value
Author(s)
Examples
Description
Imports the raw read counts from sorted and indexed bam file(s)
Usage
1
rawCounts(bamFilepath, threads = 1)
Arguments
bamFilepath
The path to the location of the bam file(s).
threads
The total number of usable threads to be used. Default is 1.
Value
Produces a RangedSummarizedExperiment. Columns are samples and the rows are cut sites. The cut site IDs are in the format chr:position-position:strand.
Author(s)
Benjamin Mayne, Sam Buckberry
Examples
1
2
my_path <- system.file("extdata", package = "msgbsR")
my_data <- rawCounts(bamFilepath = my_path)
BenjaminAdelaide/msgbsR documentation built on May 5, 2019, 2:41 p.m.
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Description Usage Arguments Value Author(s) Examples
Description
Imports the raw read counts from sorted and indexed bam file(s)
Usage
1 | rawCounts(bamFilepath, threads = 1)
|
Arguments
bamFilepath |
The path to the location of the bam file(s). |
threads |
The total number of usable threads to be used. Default is 1. |
Value
Produces a RangedSummarizedExperiment. Columns are samples and the rows are cut sites. The cut site IDs are in the format chr:position-position:strand.
Author(s)
Benjamin Mayne, Sam Buckberry
Examples
1 2 | my_path <- system.file("extdata", package = "msgbsR")
my_data <- rawCounts(bamFilepath = my_path)
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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