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

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

Author
Qiong Ding, Jinlong Zhang
Date of publication
2012-10-29 08:59:40
Maintainer
Qiong Ding <dingqiong1@gmail.com>
License
GPL-2
Version
1.0.1

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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

Files in this package

seqRFLP
seqRFLP/data
seqRFLP/data/fil.phy.rda
seqRFLP/data/fil.fas.rda
seqRFLP/data/enzdata.rda
seqRFLP/data/fil.nxs.rda
seqRFLP/NAMESPACE
seqRFLP/man
seqRFLP/man/ConvFas.Rd
seqRFLP/man/raw2Fas.Rd
seqRFLP/man/revComp.Rd
seqRFLP/man/plotenz.Rd
seqRFLP/man/rename.fas.Rd
seqRFLP/man/fil.phy.Rd
seqRFLP/man/as.fasta.Rd
seqRFLP/man/clipprobe.Rd
seqRFLP/man/enzdata.Rd
seqRFLP/man/gnames.fas.Rd
seqRFLP/man/fil.nxs.Rd
seqRFLP/man/write.fasta.Rd
seqRFLP/man/read.phy.Rd
seqRFLP/man/findprobe.Rd
seqRFLP/man/seqRFLP-package.Rd
seqRFLP/man/file.cat.Rd
seqRFLP/man/read.fasta.Rd
seqRFLP/man/enzCut.Rd
seqRFLP/man/fil.fas.Rd
seqRFLP/man/read.nxs.Rd
seqRFLP/man/dataframe2fas.Rd
seqRFLP/man/selEnz.Rd
seqRFLP/man/frag.dat.Rd
seqRFLP/inst
seqRFLP/inst/extdata
seqRFLP/inst/extdata/seqs.fasta
seqRFLP/inst/extdata/link_gcg
seqRFLP/DESCRIPTION
seqRFLP/MD5
seqRFLP/R
seqRFLP/R/plotenz.R
seqRFLP/R/frag.dat.R
seqRFLP/R/ConvFas.R
seqRFLP/R/rename.fas.R
seqRFLP/R/findprobe.R
seqRFLP/R/clipprobe.R
seqRFLP/R/as.fasta.R
seqRFLP/R/read.fasta.R
seqRFLP/R/gnames.fas.R
seqRFLP/R/revComp.R
seqRFLP/R/read.nxs.R
seqRFLP/R/write.fasta.R
seqRFLP/R/read.phy.R
seqRFLP/R/enzCut.R
seqRFLP/R/file.cat.R
seqRFLP/R/raw2Fas.R
seqRFLP/R/dataframe2fas.R
seqRFLP/R/selEnz.R