bam2coverage: Convert a bam file to coverage
In musikutiv/tsTools: Toolbox for Functional Genomics Data Processing in R
bam2coverage R Documentation
Convert a bam file to coverage
Description
Reads can optionally be filtered by a chromosome inclusion list
Single reads will be extended to the provided fragment length
Usage
bam2coverage(file.id, type = c("SINGLE", "PAIRED"), fragment.length = 200,
chr.flt = NA)
Arguments
file.id
path of the bam file
type
sequencing library type "SINGLE" or "PAIRED"
fragment.length
average chromatin fragment size, default 200
chr.flt
vector of chromosome names to be included
Value
a coverage object (RleList as returned by coverage)
musikutiv/tsTools documentation built on June 6, 2023, 1:39 a.m.
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| bam2coverage | R Documentation |
Convert a bam file to coverage
Description
Reads can optionally be filtered by a chromosome inclusion list Single reads will be extended to the provided fragment length
Usage
bam2coverage(file.id, type = c("SINGLE", "PAIRED"), fragment.length = 200,
chr.flt = NA)
Arguments
file.id |
path of the bam file |
type |
sequencing library type "SINGLE" or "PAIRED" |
fragment.length |
average chromatin fragment size, default 200 |
chr.flt |
vector of chromosome names to be included |
Value
a coverage object (RleList as returned by coverage)
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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