importUCSC: Import TE intervals in UCSC table browser format
In tanaylab/reputils: Utility functions for working with transposable elements
Description
Usage
Arguments
Value
Description
Import TE intervals from UCSC table browser
Usage
1
2
importUCSC(path = "path to UCSC RMSK file", curate = FALSE,
main_classes = TRUE, main_assembly = TRUE)
Arguments
path
Character. Path to file.
curate
Logical. If TRUE, calls 'curateTEs' to resolve overlapping TE intervals.
main_classes
Logical. If TRUE (the default), only returns TE intervals unambiguously belonging to DNA, LINE, SINE, and LTR classes.
main_assembly
Logical. If TRUE (the default), only returns TE intervals on the main chromosomes.
Value
Returns a GRanges object with TE intervals
tanaylab/reputils documentation built on Nov. 5, 2019, 9:58 a.m.
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Description Usage Arguments Value
Description
Import TE intervals from UCSC table browser
Usage
1 2 | importUCSC(path = "path to UCSC RMSK file", curate = FALSE,
main_classes = TRUE, main_assembly = TRUE)
|
Arguments
path |
Character. Path to file. |
curate |
Logical. If TRUE, calls 'curateTEs' to resolve overlapping TE intervals. |
main_classes |
Logical. If TRUE (the default), only returns TE intervals unambiguously belonging to DNA, LINE, SINE, and LTR classes. |
main_assembly |
Logical. If TRUE (the default), only returns TE intervals on the main chromosomes. |
Value
Returns a GRanges object with TE intervals
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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