rm_format: Parse a given RepeatMasker annotation file.

In karakulahlab/Tool1:

Description

This function takes RepeatMasker annotation file as input and extracts the genomic location of each TE along with repeat class and family information. The output of rm_format() function is used while searching TEs that are located in the upstream region of the genes of interest. Repeat annotation files can be downloaded from http://www.repeatmasker.org/genomicDatasets/RMGenomicDatasets.html

Usage

rm_format(filepath)

Arguments

filepath

it is a character that refers directory of downloaded repeat file.

See Also

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Examples

#Read and parse the RepeatMasker annotation file of interest.
TEffectR::rm_format(filepath="~/FilePath/hg38.fa.out.gz")

karakulahlab/Tool1 documentation built on Feb. 2, 2020, 11:05 a.m.