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TRAMPR (version 1.0-7)

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

1.0-7

License

GPL-2

Maintainer

Rich FitzJohn

Last Published

March 23rd, 2012

Functions in TRAMPR (1.0-7)

demo.knowns

Demonstration Knowns Database
remove.TRAMP.match

Mark a TRAMP Match as Ignored
absolute.min

Absolute Minimum
plot.TRAMP

Plot a TRAMP Object
TRAMP

TRFLP Analysis and Matching Program
demo.samples

Demonstration Samples Database
build.knowns

Automatically Build Knowns Database
update.TRAMP

Interactively Alter a TRAMP Object
create.diffsmatrix

Calculate Matrix of Distances between Peaks
group.knowns

Knowns Clustering
combine

Combine Two Objects
rebuild.TRAMP

Rebuild a TRAMP Object
TRAMPsamples

TRAMPsamples Objects
combine.TRAMPsamples

Combine TRAMPsamples Objects
read.abi

Read ABI Output Files
plot.TRAMPknowns

Summary Plot of Knowns Data
load.abi

Load ABI Output Files
plot.TRAMPsamples

Plot a TRAMPsamples Object
TRAMPknowns

TRAMPknowns Objects
summary.TRAMP

Create Presence/Absence Matrices from TRAMP Objects
add.known

Add Knowns To TRAMPknowns Databases
TRAMPindexing

Index (Subset) TRAMPsamples and TRAMPknowns Objects
classify

Value Matching for Data Frames
TRAMPR-package

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

Read/Write TRAMPknowns and TRAMPsamples Objects