seqRFLP (version 1.0.1)

frag.dat: Reports for simulated RFLP cutting pattern

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.

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.

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.

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)