Convert non-bisulfite sequences to bisulfite sequences.

Description

Bisulfite sequences are the bisulfite treated DNA sequences where all cytosines except cytosine from CpG sites are converted to thymie. This technique is used to determine pattern of methylation. This function convert all cytosine except cytosines from CpG sites to thymine.

Usage

bconv(fasta_file, out_file = "output.fasta")

Arguments

Value

Fasta File

Author(s)

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

Maintainer: Muhammad Ahmer Jamil engr.ahmerjamil@gmail.com

Examples

input =  system.file("extdata", "bisulfite.fasta", package = "MethTargetedNGS")
bconv(fasta_file = input, out_file = "output.fasta")

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/bconv.Rd_%03d_medium.png", width=480, height=480)
> ### Name: bconv
> ### Title: Convert non-bisulfite sequences to bisulfite sequences.
> ### Aliases: bconv
> ### Keywords: Bisulfite Conversion Methylation
> 
> ### ** Examples
> 
> input =  system.file("extdata", "bisulfite.fasta", package = "MethTargetedNGS")
> bconv(fasta_file = input, out_file = "output.fasta")
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>