posMaskedSeq {GeneR}R Documentation

Get all masked regions

Description

This function return a matrix of masked postions from a fasta file. Masked regions are identified by lower case in fasta file.

Usage

posMaskedSeq(file, name = NA, length = 10000)

Arguments

file Fasta file path
name Name of sequence (if not: the first sequence from fasta file)
length Maximum number of regions to retrieve (default: 10000)

Value

a matrix of class intervals, of size nx2.

Author(s)

Odile Rogier

Examples

## Make a dummy sequence
s <- "ATGCtgTGTTagtacATTGGGTTTaAAA"
placeString(s,upper=FALSE)
writeFasta(file="toto.fa")
posMaskedSeq("toto.fa")


[Package GeneR version 1.4.2 Index]