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TRAMPR (version 1.0-6)

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

1.0-6

License

GPL-2

Maintainer

Rich FitzJohn

Last Published

October 15th, 2009

Functions in TRAMPR (1.0-6)

TRAMPindexing

Index (Subset) TRAMPsamples and TRAMPknowns Objects
classify

Value Matching for Data Frames
create.diffsmatrix

Calculate Matrix of Distances between Peaks
TRAMPknowns

TRAMPknowns Objects
TRAMPsamples

TRAMPsamples Objects
summary.TRAMP

Create Presence/Absence Matrices from TRAMP Objects
TRAMP

TRFLP Analysis and Matching Program
demo.knowns

Demonstration Knowns Database
add.known

Add Knowns To TRAMPknowns Databases
plot.TRAMPsamples

Plot a TRAMPsamples Object
build.knowns

Automatically Build Knowns Database
rebuild.TRAMP

Rebuild a TRAMP Object
update.TRAMP

Interactively Alter a TRAMP Object
read.write

Read/Write TRAMPknowns and TRAMPsamples Objects
group.knowns

Knowns Clustering
plot.TRAMP

Plot a TRAMP Object
load.abi

Load ABI Output Files
remove.TRAMP.match

Mark a TRAMP Match as Ignored
combine.TRAMPsamples

Combine TRAMPsamples Objects
TRAMPR-package

The TRAMPR Package (TRFLP Analysis and Matching Package for R)
read.abi

Read ABI Output Files
plot.TRAMPknowns

Summary Plot of Knowns Data
absolute.min

Absolute Minimum
demo.samples

Demonstration Samples Database
combine

Combine Two Objects