blatListedSet: Align a listed DNAStringSet to a reference using gfClient or...
In hiReadsProcessor: Functions to process LM-PCR reads from 454/Illumina data
Description
Usage
Arguments
Value
See Also
View source: R/hiReadsProcessor.R
Description
Align sequences from a listed DNAStringSet object returned from
extractSeqs to an indexed reference genome using
gfServer/gfClient protocol or using standalone BLAT and return the psl file
as a GRanges object. This function heavily relies on defaults of
blatSeqs.
Usage
1
blatListedSet(dnaSetList = NULL, ...)
Arguments
dnaSetList
DNAStringSet object containing sequences to be aligned against the reference.
...
parameters to be passed to blatSeqs.
Value
a list of GRanges object reflecting psl file type per set of sequences.
See Also
pairwiseAlignSeqs, vpairwiseAlignSeqs,
startgfServer, stopgfServer,
blatSeqs, read.psl,
pslToRangedObject, read.blast8
hiReadsProcessor documentation built on Nov. 8, 2020, 5:43 p.m.
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Description Usage Arguments Value See Also
View source: R/hiReadsProcessor.R
Description
Align sequences from a listed DNAStringSet object returned from
extractSeqs to an indexed reference genome using
gfServer/gfClient protocol or using standalone BLAT and return the psl file
as a GRanges object. This function heavily relies on defaults of
blatSeqs.
Usage
1 | blatListedSet(dnaSetList = NULL, ...)
|
Arguments
dnaSetList |
DNAStringSet object containing sequences to be aligned against the reference. |
... |
parameters to be passed to |
Value
a list of GRanges object reflecting psl file type per set of sequences.
See Also
pairwiseAlignSeqs, vpairwiseAlignSeqs,
startgfServer, stopgfServer,
blatSeqs, read.psl,
pslToRangedObject, read.blast8
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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