extract the gene/family/class TE information from repeatmasker gtf

to extract TE id/family/class information and to prepare data for visualize the abundance of TEs using pie chart (refer to pieTE())

Usage

saveTErmsk(rmskGTF, fileName = FALSE)

Arguments

rmskGTF

/path/filename of your transposable element rmsk gtf

fileName

provide file name if you want to save your result instead of just returning it.

Value

a TE reference dataframe include gene_id, family_id and class_id

Examples