seqRFLP: Simulation and visualization of restriction enzyme cutting pattern from DNA sequences.
Version 1.0.1

This package includes functions for handling DNA sequences, especially simulated RFLP and TRFLP pattern based on selected restriction enzyme and DNA sequences.

Browse man pages Browse package API and functions Browse package files

AuthorQiong Ding, Jinlong Zhang
Date of publication2012-10-29 08:59:40
MaintainerQiong Ding <dingqiong1@gmail.com>
LicenseGPL-2
Version1.0.1
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("seqRFLP")

Man pages

as.fasta: Coerce "phy" or "nex" objects to fasta format.
clipprobe: Finding the sequences that could be clipped given two...
ConvFas: Convert files to fasta format
dataframe2fas: Convert dataframe to fasta format
enzCut: Restriction enzyme cutting pattern
enzdata: The restriction enzyme datasets.
file.cat: Copy or concatenate files to one.
fil.fas: Fasta data example.
fil.nxs: Internal nexus data.
fil.phy: Internal phylip format data
findprobe: Find probes matching sites
frag.dat: Reports for simulated RFLP cutting pattern
gnames.fas: Get the names of sequences from fasta objects.
plotenz: Plotting the simulated RFLP or TRFLP pattern
raw2Fas: Read and converting raw DNA files to fasta format.
read.fasta: Read fasta file
read.nxs: Read nexus file
read.phy: Read phylip file
rename.fas: Change the sequence names of fasta objects.
revComp: Reverse complement sequence
selEnz: Selecting restriction enzyme
seqRFLP-package: Simulation and visualization of Restriction Fragment Length...
write.fasta: Write fasta format object to file

Functions

ConvFas Man page Source code
as.fasta Man page Source code
clipprobe Man page Source code
dataframe2fas Man page Source code
enzCut Man page Source code
enzdata Man page
fil.fas Man page
fil.nxs Man page
fil.phy Man page
file.cat Man page Source code
findprobe Man page Source code
frag.dat Man page Source code
gnames.fas Man page Source code
plotenz Man page Source code
raw2Fas Man page Source code
read.fasta Man page Source code
read.nxs Man page Source code
read.phy Man page Source code
rename.fas Man page Source code
revComp Man page Source code
selEnz Man page Source code
seqRFLP Man page
seqRFLP-package Man page
write.fasta Man page Source code

Files

data
data/fil.phy.rda
data/fil.fas.rda
data/enzdata.rda
data/fil.nxs.rda
NAMESPACE
man
man/ConvFas.Rd
man/raw2Fas.Rd
man/revComp.Rd
man/plotenz.Rd
man/rename.fas.Rd
man/fil.phy.Rd
man/as.fasta.Rd
man/clipprobe.Rd
man/enzdata.Rd
man/gnames.fas.Rd
man/fil.nxs.Rd
man/write.fasta.Rd
man/read.phy.Rd
man/findprobe.Rd
man/seqRFLP-package.Rd
man/file.cat.Rd
man/read.fasta.Rd
man/enzCut.Rd
man/fil.fas.Rd
man/read.nxs.Rd
man/dataframe2fas.Rd
man/selEnz.Rd
man/frag.dat.Rd
inst
inst/extdata
inst/extdata/seqs.fasta
inst/extdata/link_gcg
DESCRIPTION
MD5
R
R/plotenz.R
R/frag.dat.R
R/ConvFas.R
R/rename.fas.R
R/findprobe.R
R/clipprobe.R
R/as.fasta.R
R/read.fasta.R
R/gnames.fas.R
R/revComp.R
R/read.nxs.R
R/write.fasta.R
R/read.phy.R
R/enzCut.R
R/file.cat.R
R/raw2Fas.R
R/dataframe2fas.R
R/selEnz.R
seqRFLP documentation built on May 29, 2017, 7:06 p.m.