posMaskedSeq {GeneR} | R Documentation |
This function return a matrix of masked postions from a fasta file. Masked regions are identified by lower case in fasta file.
posMaskedSeq(file, name = NA, length = 10000)
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) |
a matrix of class intervals, of size nx2.
Odile Rogier
## Make a dummy sequence s <- "ATGCtgTGTTagtacATTGGGTTTaAAA" placeString(s,upper=FALSE) writeFasta(file="toto.fa") posMaskedSeq("toto.fa")