Last data update: 2014.03.03
R: Align sequences with the reference sequence using...
Align sequences with the reference sequence using pairwiseAlignment function from BioStrings
Description
This function allow users to align pool of sequences to the reference sequence.
Usage
methAlign(sequence_fasta, ref_seq, sub_mat = FALSE, align_type = "local")
Arguments
sequence_fasta
String value naming an input fasta file. Single sequence or Multiple sequences in a single fasta file
ref_seq
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.
sub_mat
Substitution matrix for the alignment.
align_type
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"
Value
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.
Note
This function need some time to process depending on the number of sequences in fasta file
Author(s)
Muhammad Ahmer Jamil, Prof. Holger Frohlich, Priv.-Doz. Dr. Osman El-Maarri
Maintainer: Muhammad Ahmer Jamil engr.ahmerjamil@gmail.com
See Also
compare_samples
Examples
healthy = system.file("extdata", "Healthy.fasta", package = "MethTargetedNGS")
reference = system.file("extdata", "Reference.fasta", package = "MethTargetedNGS")
methAlign(healthy,reference)
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(MethTargetedNGS)
Loading required package: stringr
Loading required package: seqinr
Loading required package: gplots
Attaching package: 'gplots'
The following object is masked from 'package:stats':
lowess
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, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:gplots':
space
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: IRanges
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:seqinr':
translate
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/MethTargetedNGS/methAlign.Rd_%03d_medium.png", width=480, height=480)
> ### Name: methAlign
> ### Title: Align sequences with the reference sequence using
> ### pairwiseAlignment function from BioStrings
> ### Aliases: methAlign
> ### Keywords: Sequence Alignment Methylation Analysis
>
> ### ** Examples
>
> healthy = system.file("extdata", "Healthy.fasta", package = "MethTargetedNGS")
> reference = system.file("extdata", "Reference.fasta", package = "MethTargetedNGS")
> methAlign(healthy,reference)
Time difference of 1.32 secs
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> dev.off()
null device
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