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RFLPtools (version 2.0)

Tools to Analyse RFLP Data

Description

Provides functions to analyse DNA fragment samples (i.e. derived from RFLP-analysis) and standalone BLAST report files (i.e. DNA sequence analysis).

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Version

Install

install.packages('RFLPtools')

Monthly Downloads

217

Version

2.0

License

LGPL-3

Maintainer

Matthias Kohl

Last Published

February 8th, 2022

Functions in RFLPtools (2.0)

RFLPdata

Example data set for RFLP data
FragMatch

Compute matches for RFLP data via FragMatch.
RFLPlod

Remove bands below LOD
RFLPdist2

Compute distances for RFLP data.
RFLPplot

Function to plot RFLP data.
RFLPdist2ref

Compute distance between RFLP data and RFLP reference data.
RFLPdist

Compute distances for RFLP data.
RFLPtools-package

Tools To Analyse RFLP-Data
BLASTdata

Example data set for BLAST data
RFLPcombine

Combine RFLP data sets
read.blast

Read BLAST data
simMatrix

Similarity matrix for BLAST data.
simulateRFLPdata

Simulate RFLP data.
read.rflp

Read RFLP data
refDataGerm

Example data set from GERM software
sim2dist

Convert similarity matrix to dist object.
germ

Compute matches for RFLP data via GERM.
linCombDist

Linear Combination of Distances
nrBands

Function to compute number of bands.
newDataGerm

Example data set from GERM software
write.hclust

Cut a hierarchical cluster tree and write cluster identifiers to a text file.
RFLPrefplot

Function for a visual comparison of RFLP samples with reference samples.
diffDist

Distance Matrix Computation
RFLPref

Example data set for RFLP reference
RFLPqc

Quality control for RFLP data