gseq.create_track: Create sequence tracks for misha database

In tanaylab/misha.ext: A home to functions that extend the misha package

Create sequence tracks for misha database

Description

Create tracks based on the presence of specific sequences.

Usage

gseq.create_track(s, track, strand = 1, intervals = gintervals.all())

Arguments

s	sequence to look for. can be a regex.
track	name of the track to create
strand	strand of the sequences
intervals	intervals set

Examples

## Not run: 
gseq.create_track("C", "seq.C")
gseq.create_track("T", "seq.T")
gseq.create_track("CG", "seq.CG") # genome CpGs
gseq.create_track("[GC]", "seq.G_or_C") # C or G (for GC content calculations)

# create all dinucleotide tracks
dinucs <- expand.grid(c("T", "C", "G", "A"), c("T", "C", "G", "A"))
dinucs <- apply(dinucs, 1, paste, collapse = "")
for (dinuc in dinucs) {
    message(dinuc)
    gseq.create_track(dinuc, paste0("seq.", dinuc))
}

## End(Not run)

tanaylab/misha.ext documentation built on Sept. 18, 2024, 2:53 a.m.