methAlign: Align sequences with the reference sequence using...

Description Usage Arguments Value Note Author(s) See Also Examples

View source: R/sequenceAlignment.R


This function allow users to align pool of sequences to the reference sequence.


methAlign(sequence_fasta, ref_seq, sub_mat = FALSE, align_type = "local")



String value naming an input fasta file. Single sequence or Multiple sequences in a single fasta file


String value naming an input fasta file. Single reference sequence is requried. If multiple sequences were passed only first sequence will be considered as reference.


Substitution matrix for the alignment.


type of alignment. One of "global", "local", "overlap", "global-local", and "local-global" where

"global" = align whole strings with end gap penalties,

"local" = align string fragments,

"overlap" = align whole strings without end gap penalties,

"global-local" = align whole strings in pattern with consecutive subsequence of subject,

"local-global" = align consecutive subsequence of pattern with whole strings in subject.

Default is "local"


Methylation Matrix. Number of rows represents number of reads in sequence fasta file and number of columns represents number of CpG sites in reference fasta sequence. Only Cytosine of CpG site was observed in the table whether it is methylated or unmethylated.


This function need some time to process depending on the number of sequences in fasta file


Muhammad Ahmer Jamil, Prof. Holger Frohlich, Priv.-Doz. Dr. Osman El-Maarri

Maintainer: Muhammad Ahmer Jamil

See Also



healthy = system.file("extdata", "Healthy.fasta", package = "MethTargetedNGS")
reference = system.file("extdata", "Reference.fasta", package = "MethTargetedNGS")

Example output

Loading required package: stringr
Loading required package: seqinr
Loading required package: gplots

Attaching package: 'gplots'

The following object is masked from 'package:stats':


Loading required package: Biostrings
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,, basename, cbind, colMeans, colSums, colnames,
    dirname,, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax,, pmin,, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:gplots':


The following object is masked from 'package:base':


Loading required package: IRanges
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:seqinr':


The following object is masked from 'package:base':


Time difference of 1.98 secs
               1   2   3   4   5   6   7   8   9   10  11  12  13  14 
HJ4Y1TH02DX53A "C" "C" "T" "C" "C" "C" "C" "C" "C" "C" "C" "C" "C" "T"
HJ4Y1TH02EMRDU "T" "C" "C" "C" "C" "C" "C" "C" "C" "T" "C" "C" "T" "C"
HJ4Y1TH02DA2Z9 "T" "C" "C" "C" "C" "C" "C" "C" "C" "C" "C" "C" "T" "T"
HJ4Y1TH02EDLUP "T" "C" "C" "C" "C" "C" "C" "C" "C" "C" "T" "C" "C" "C"
HJ4Y1TH02ELST9 "T" "C" "C" "C" "C" "C" "C" "C" "C" "C" "C" "C" "C" "C"
HJ4Y1TH02EJJ1G "C" "C" "C" "C" "C" "C" "C" "C" "C" "C" "C" "C" "C" "C"
HJ4Y1TH02DPUV1 "T" "C" "C" "C" "C" "C" "C" "C" "T" "T" "T" "T" "T" "C"
HJ4Y1TH02D2MOC "C" "C" "C" "C" "C" "C" "C" "C" "C" "T" "C" "C" "C" "C"
HJ4Y1TH02DYX62 "T" "T" "C" "C" "C" "C" "C" "C" "C" "T" "C" "C" "C" "C"
HJ4Y1TH02C37Y4 "T" "-" "C" "C" "C" "C" "C" "C" "C" "C" "C" "C" "C" "T"
HJ4Y1TH02DGPVU "T" "C" "T" "T" "T" "T" "T" "C" "C" "T" "C" "T" "C" "T"
HJ4Y1TH02DBSO3 "T" "C" "C" "C" "C" "C" "C" "C" "C" "C" "C" "C" "C" "C"
HJ4Y1TH02DNNLI "C" "C" "C" "C" "C" "C" "C" "C" "C" "C" "C" "C" "C" "C"
HJ4Y1TH02DRFAD "C" "C" "C" "C" "C" "C" "C" "T" "C" "C" "C" "T" "C" "T"
HJ4Y1TH02DT5D1 "C" "C" "C" "C" "C" "C" "C" "T" "T" "C" "C" "C" "C" "C"
HJ4Y1TH02D149G "C" "C" "C" "C" "C" "C" "C" "C" "C" "C" "C" "C" "C" "C"
HJ4Y1TH02D8VOW "C" "C" "C" "C" "C" "C" "C" "T" "T" "C" "C" "C" "C" "C"
HJ4Y1TH02DKAL3 "C" "C" "C" "C" "C" "C" "T" "C" "C" "C" "C" "C" "T" "T"
HJ4Y1TH02EF3HZ "C" "C" "C" "C" "C" "C" "C" "C" "C" "C" "C" "C" "C" "C"
HJ4Y1TH02EPGZN "C" "C" "C" "C" "C" "C" "C" "C" "C" "T" "C" "C" "C" "C"
HJ4Y1TH02DQYYV "T" "C" "C" "C" "C" "C" "C" "T" "C" "C" "C" "C" "C" "C"
HJ4Y1TH02C098E "C" "C" "T" "T" "T" "T" "T" "C" "C" "C" "C" "C" "C" "C"
HJ4Y1TH02EM5MO "C" "C" "C" "C" "C" "C" "C" "C" "C" "C" "C" "C" "C" "C"
HJ4Y1TH02DNIBF "C" "C" "C" "C" "C" "C" "C" "C" "C" "C" "C" "C" "C" "C"
HJ4Y1TH02DR0A5 "C" "C" "C" "C" "C" "C" "C" "C" "C" "C" "C" "C" "T" "C"

MethTargetedNGS documentation built on Nov. 8, 2020, 8:10 p.m.