strandedBamImport: Stranded bam import
In PietaSchofield/plibb: Pieta Schofield's repository of former useful R functions
Description
A function to extract reads from a stranded RNA-seq BAM file. Intended to be used as a custom
importFunction in the DataTrack constructor of Bioconductor's Gviz package. With properly
stranded data this allows the plotting of coverage tracks from each strand of the genome.
6 Nov 2014 - bensidders at gmail dot com
UPDATE: 10 Sep 2015: The funciton can now plot data from libraries created in either
orientation. Due to the manner in which Gviz calls <c2><a7>this function, you need to specify the
library orientation with a global variable "libType" to be one of "fr-firststrand" or
"fr-secondstrand".
Usage
1
strandedBamImport(file, selection)
PietaSchofield/plibb documentation built on May 6, 2019, 6:45 p.m.
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Description
A function to extract reads from a stranded RNA-seq BAM file. Intended to be used as a custom importFunction in the DataTrack constructor of Bioconductor's Gviz package. With properly stranded data this allows the plotting of coverage tracks from each strand of the genome. 6 Nov 2014 - bensidders at gmail dot com UPDATE: 10 Sep 2015: The funciton can now plot data from libraries created in either orientation. Due to the manner in which Gviz calls <c2><a7>this function, you need to specify the library orientation with a global variable "libType" to be one of "fr-firststrand" or "fr-secondstrand".
Usage
1 | strandedBamImport(file, selection)
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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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