strandedScanBamParam: create coverage scanbamparam object
In cmatKhan/brentlabRnaSeqTools: A Collection of Functions to Interact with the Brentlab RNASeq Database
Description
Usage
Arguments
Value
See Also
Description
helper function to create ScanBamParam object with appropriate strandedness information
Usage
1
strandedScanBamParam(locus_granges, strandedness, quality_threshold = 20L)
Arguments
locus_granges
a granges object for a given gene (or some other feature on only one strand)
strandedness
one of c("reverse", "same", "unstranded")
quality_threshold
quality threshold above which reads will be considered. 20l is default, which is
chosen b/c it is the default for HTSeq
Value
a ScanBamParam object with certain configured options, as well as some reasonable defaults, to filter
a bam file for reads of interest based on the strandedness (protocol) of the library prep.
See Also
cmatKhan/brentlabRnaSeqTools documentation built on Nov. 17, 2021, 5:47 a.m.
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Description Usage Arguments Value See Also
Description
helper function to create ScanBamParam object with appropriate strandedness information
Usage
1 | strandedScanBamParam(locus_granges, strandedness, quality_threshold = 20L)
|
Arguments
locus_granges |
a granges object for a given gene (or some other feature on only one strand) |
strandedness |
one of c("reverse", "same", "unstranded") |
quality_threshold |
quality threshold above which reads will be considered. 20l is default, which is chosen b/c it is the default for HTSeq |
Value
a ScanBamParam object with certain configured options, as well as some reasonable defaults, to filter a bam file for reads of interest based on the strandedness (protocol) of the library prep.
See Also
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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