read.alignfile: Read .align file from RepeatMasker

In FemeniasM/ExplorATEproject: Explore Active Transposable Elements from RNAseq data

Read .align file from RepeatMasker

Description

read .align file from RepeatMasker

Usage

read.alignfile(file, average = F, by = c("seqID", "classRep"))

Arguments

file	.align file
average	logical vector indicating if the mean should be taken
by	if average = TRUE, then it must be indicated if the average is taken by sequences, by = "seqID", or by repetition class, by = "classRep".

Details

reads the RepeatMasker .align file and returns a data.frame with the sequence ID, the repetitions class, and the sequence divergence respect to the reference sequence in Kimura 2-parameter distances. If average = TRUE return a vector with means by sequences (by = "seqID") or by repetition class (by = "classRep") as indicated.

FemeniasM/ExplorATEproject documentation built on Nov. 30, 2022, 5:26 p.m.