prepareRMSK: Prepare a table from two species RepeatMakser track from UCSC...

In ferygood/TEKRABber: An R package estimates the correlations of orthologs and transposable elements between two species

Prepare a table from two species RepeatMakser track from UCSC genome Table

Description

create a table to the rmsk argument in orthologScale(). Before version 1.8, TEKRABber requires user to prepare this table by themselves and this function can help user automatically get the RepeatMasker table from UCSC. The arguments required are the abbreviation of the version of reference (case-sensitive). For example, "hg38" for human. Note: currently only 91 genomes provided. Check if the reference exists with GenomeInfoDb::registered_UCSC_genomes().

Usage

prepareRMSK(refSpecies, compareSpecies)

Arguments

refSpecies	the version of reference species, i.e. hg38
compareSpecies	the version of compared species, i.e. panTro6

Value

Dataframe with four columns: repName, repClass, rLen and cLen

Examples

df_rmsk <- prepareRMSK(refSpecies = "hg38", compareSpecies = "panTro6") 

ferygood/TEKRABber documentation built on July 31, 2024, 6:36 p.m.