DottedAlignment: Align haplotypes into a dotted alignment

Description Usage Arguments Value Author(s) See Also Examples

Description

Given an alignment, it takes the first sequence as reference, and depicts all equivalences in the alignment as dots, leaving only the variants with respect to the reference.

Usage

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Arguments

hseqs

DNAStringSet or AAStringSet with haplotype sequences.

Value

A character string vector of the alignment, with dots in the conserved positions.

Author(s)

Mercedes Guerrero-Murillo and Josep Gregori

See Also

ReadAmplSeqs

Examples

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filepath<-system.file("extdata","ToyData_10_50_1000.fna", package="QSutils")
lst <- ReadAmplSeqs(filepath,type="DNA")
strs <- DottedAlignment(lst$hseqs)

# Create a data frame to visualize the result.
data.frame(Hpl=strs,stringsAsFactors=FALSE)

VHIRHepatiques/QSutils documentation built on May 8, 2019, 1:44 p.m.