bconv: Convert non-bisulfite sequences to bisulfite sequences.

In MethTargetedNGS: Perform Methylation Analysis on Next Generation Sequencing Data

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

fasta_file	: Input fasta file for conversion
out_file	: String value naming an output file. Default is output.fasta

Value

Fasta File

Author(s)

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

Maintainer: Muhammad Ahmer Jamil [e-mail]

Examples

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

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':

    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, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, 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,
    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':

    space

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

    expand.grid

Loading required package: IRanges
Loading required package: XVector

Attaching package: 'Biostrings'

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

    translate

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

    strsplit

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