addpos2string: addpos2string

In kullrich/MSA2dist: MSA2dist calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis

addpos2string

Description

This function adds GenomicRanges information, CHROM, START and END to a DNAStringSet or an AAStringSet and puts them into the metadata information. This information can be used to find overlaps with a chromosome wide mask.

Usage

addpos2string(seq, chrom = NULL, start = NULL, end = NULL)

Arguments

seq	DNAStringSet or AAStringSet [mandatory]
chrom	chromosome name [mandatory]
start	start position [mandatory]
end	end position [mandatory]

Value

An object of class DNAStringSet or AAStringSet

Author(s)

Kristian K Ullrich

See Also

addmask2string, addregion2string, addpop2string

Examples

## load example sequence data
data(iupac, package="MSA2dist")
## add position
iupac <- iupac |> addpos2string(chrom="chr1", start=1, end=1000)
#(iupac |> slot("metadata"))$GRanges
iupac |> getpos()

kullrich/MSA2dist documentation built on Nov. 14, 2024, 5:39 p.m.