parseCAGEscanBlocksToGrangeTSS: parseCAGEscanBlocksToGrangeTSS
In CAGEr: Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining
Description
Usage
Arguments
Value
See Also
Examples
Description
Parse a string describing a block in a CAGEscan molecule, as output by
the "CAGEscan 3.0" pipeline.
Usage
1
parseCAGEscanBlocksToGrangeTSS(blocks)
Arguments
blocks
A character string representing a block in a CAGEscan molecule.
Value
A GRanges object representing a TSS.
In CAGEscan molecules, blocks are separated by ‘|’, ‘,’ or
‘;’ for gap of coverage, splice junction (confident) and splice
junction (maybe) respectively. Strand is "+" if first coordinate is lower
than the second one, and "-" otherwise.
See Also
import.CAGEscanMolecule
Examples
1
2
3
4
5
6
7
myMolecule <- paste0( "chr11:66268633-66268693,"
, "chr11:66271796-66271869;"
, "chr11:66272156-66272252|"
, "chr11:66272364-66272460")
myFirstBlock <- sub("[,;|].*", "", myMolecule)
CAGEr:::parseCAGEscanBlocksToGrangeTSS(myFirstBlock)
CAGEr documentation built on Jan. 17, 2021, 2 a.m.
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Description Usage Arguments Value See Also Examples
Description
Parse a string describing a block in a CAGEscan molecule, as output by the "CAGEscan 3.0" pipeline.
Usage
1 | parseCAGEscanBlocksToGrangeTSS(blocks)
|
Arguments
blocks |
A character string representing a block in a CAGEscan molecule. |
Value
A GRanges object representing a TSS.
In CAGEscan molecules, blocks are separated by ‘|’, ‘,’ or ‘;’ for gap of coverage, splice junction (confident) and splice junction (maybe) respectively. Strand is "+" if first coordinate is lower than the second one, and "-" otherwise.
See Also
import.CAGEscanMolecule
Examples
1 2 3 4 5 6 7 | myMolecule <- paste0( "chr11:66268633-66268693,"
, "chr11:66271796-66271869;"
, "chr11:66272156-66272252|"
, "chr11:66272364-66272460")
myFirstBlock <- sub("[,;|].*", "", myMolecule)
CAGEr:::parseCAGEscanBlocksToGrangeTSS(myFirstBlock)
|
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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