pullRegion: Pull counts from a bam file for target region
In sherrillmix/dnar: Miscellaneous functions to deal with bioinformatic analyses
pullRegion R Documentation
Pull counts from a bam file for target region
Description
Pull counts from a bam file for target region
Usage
pullRegion(
reg,
files,
bam2depthBinary = "./bam2depth",
fillMissingZeros = TRUE
)
Arguments
reg
region in the format "chrX:123545-123324"
files
bam files to pull the counts from
bam2depthBinary
bam2depth executable file
fillMissingZeros
if TRUE fill in uncovered positions with zeros otherwise may be left out of output by bam2depth
Value
data.frame with columns chr, pos and counts
sherrillmix/dnar documentation built on July 18, 2022, 10:07 p.m.
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| pullRegion | R Documentation |
Pull counts from a bam file for target region
Description
Pull counts from a bam file for target region
Usage
pullRegion( reg, files, bam2depthBinary = "./bam2depth", fillMissingZeros = TRUE )
Arguments
reg |
region in the format "chrX:123545-123324" |
files |
bam files to pull the counts from |
bam2depthBinary |
bam2depth executable file |
fillMissingZeros |
if TRUE fill in uncovered positions with zeros otherwise may be left out of output by bam2depth |
Value
data.frame with columns chr, pos and counts
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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