rm_format: Parse a given RepeatMasker annotation file.

In ferygood/TEffectR_yao:

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

.

Examples

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

ferygood/TEffectR_yao documentation built on Jan. 1, 2021, 1:20 a.m.