frag.dat: Reports for simulated RFLP cutting pattern

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

Description

Generating reports of simulated RFLP cutting patterns.

Usage

frag.dat(fil, enznames, enzdata)

Arguments

fil	sequence data in class fasta.
enznames	selected enzyme name from enzdata.
enzdata	a dataframe contained enzyme information.

Details

Given the name of restriction enzyme, the function will give the simulated RFLP pattern. The input sequences must be a fasta format object, which means it must be first converted to class "fasta". Users are encouraged to use read.fasta, read.phy, read.nxs to read files from local machine, and converted the data to class fasta using as.fasta.

Value

This function returns to a dataframe which including the following columns. with rownames the sequence name.

enznames	enzyme name
recogSite	The recognition site of the specified enzyme.
cutting_Site	The cutting site number on the sequence from 5' to 3'.
fragment_Length	The length of each fragments from 5' to 3'
T5	Length of the 5' terminal fragment from the original sequence.
T3	Length of the 3' terminal fragment from the original sequence.

Note

To be added.

Author(s)

Qiong Ding [e-mail]

References

None.

Examples

### fragdat() example
data(enzdata)
data(fil.phy)
fas <- ConvFas(fil = fil.phy, type = "phy")
frag.dat(fil = fas, enznames = "EcoRI", enzdata = enzdata)

seqRFLP documentation built on May 2, 2019, 6:02 a.m.