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TRAMPR (version 1.0-5)

TRFLP Analysis and Matching Package for R

Description

TRAMPR is an R package for matching terminal restriction fragment length polymorphism (TRFLP) profiles between unknown samples and a database of knowns. TRAMPR facilitates analysis of many unknown profiles at once, and provides tools for working directly with electrophoresis output through to generating summaries suitable for community analyses with R's rich set of statistical functions. TRAMPR also resolves the issues of multiple TRFLP profiles within a species, and shared TRFLP profiles across species.

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Version

Install

install.packages('TRAMPR')

Monthly Downloads

2,026

Version

1.0-5

License

GPL-2

Maintainer

Rich FitzJohn

Last Published

May 24th, 2009

Functions in TRAMPR (1.0-5)

rebuild.TRAMP

Rebuild a TRAMP Object
TRAMPknowns

TRAMPknowns Objects
absolute.min

Absolute Minimum
add.known

Add Knowns To TRAMPknowns Databases
TRAMPsamples

TRAMPsamples Objects
load.abi

Load ABI Output Files
combine.TRAMPsamples

Combine TRAMPsamples Objects
demo.knowns

Demonstration Knowns Database
build.knowns

Automatically Build Knowns Database
TRAMPR-package

The TRAMPR Package (TRFLP Analysis and Matching Package for R)
plot.TRAMP

Plot a TRAMP Object
combine

Combine Two Objects
TRAMP

TRFLP Analysis and Matching Program
classify

Value Matching for Data Frames
create.diffsmatrix

Calculate Matrix of Distances between Peaks
plot.TRAMPknowns

Summary Plot of Knowns Data
remove.TRAMP.match

Mark a TRAMP Match as Ignored
TRAMPindexing

Index (Subset) TRAMPsamples and TRAMPknowns Objects
demo.samples

Demonstration Samples Database
group.knowns

Knowns Clustering
summary.TRAMP

Create Presence/Absence Matrices from TRAMP Objects
read.write

Read/Write TRAMPknowns and TRAMPsamples Objects
plot.TRAMPsamples

Plot a TRAMPsamples Object
update.TRAMP

Interactively Alter a TRAMP Object
read.abi

Read ABI Output Files