getReadLength: get the read length from a bam file
In jrboyd/peakrefine: Peak Refinement Metric Gathering and Evalutation by Motif Enrichment
Description
Usage
Arguments
Value
Examples
View source: R/functions_crossCorrRle.R
Description
get the read length from a bam file
Usage
1
getReadLength(bam_file, query_gr)
Arguments
bam_file
character. Path to .bam file, must have index at .bam.bai.
query_gr
GRanges. Regions to calculate cross correlation for. Only first 10 actually used.
Value
numeric. the most common read length observed in bam.
Examples
1
2
3
4
bam_file = system.file("extdata", "MCF10A_CTCF.random5.bam", package = "peakrefine")
np = system.file("extdata", "MCF10A_CTCF.random5.narrowPeak", package = "peakrefine")
query_gr = rtracklayer::import(np, format = "narrowPeak")
getReadLength(bam_file, query_gr)
jrboyd/peakrefine documentation built on July 30, 2020, 7:13 p.m.
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Description Usage Arguments Value Examples
View source: R/functions_crossCorrRle.R
Description
get the read length from a bam file
Usage
1 | getReadLength(bam_file, query_gr)
|
Arguments
bam_file |
character. Path to .bam file, must have index at .bam.bai. |
query_gr |
GRanges. Regions to calculate cross correlation for. Only first 10 actually used. |
Value
numeric. the most common read length observed in bam.
Examples
1 2 3 4 | bam_file = system.file("extdata", "MCF10A_CTCF.random5.bam", package = "peakrefine")
np = system.file("extdata", "MCF10A_CTCF.random5.narrowPeak", package = "peakrefine")
query_gr = rtracklayer::import(np, format = "narrowPeak")
getReadLength(bam_file, query_gr)
|
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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