rphast (version 1.0)

offset.msa: MSA Index Offset

Description

Returns the offset of the first position in an alignment from some reference sequence.

Usage

offset.msa(msa)

Arguments

msa

an MSA object

Value

• The difference between the first position in an alignment from the beginning of a chromosome.

Examples

m <- msa(seqs=c("A--ACGTAT", "AG-AGGTAA", "AGGAGGTAG"),
         names=c("human", "mouse", "rat"))
offset.msa(m)
m <- msa(seqs=c("A--ACGTAT", "AG-AGGTAA", "AGGAGGTAG"),
         names=c("human", "mouse", "rat"), offset=500000)
offset.msa(m)