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TRAMPR

'TRFLP' Analysis and Matching Package for R

Matching terminal restriction fragment length polymorphism ('TRFLP') profiles between unknown samples and a database of known samples. '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.

Functions (25)

TRFLP Analysis and Matching Program

TRAMPR-package

The TRAMPR Package (TRFLP Analysis and Matching Package for R)

TRAMPindexing

Index (Subset) TRAMPsamples and TRAMPknowns Objects

TRAMPknowns

TRAMPknowns Objects

TRAMPsamples

TRAMPsamples Objects

absolute.min

Absolute Minimum

Add Knowns To TRAMPknowns Databases

build.knowns

Automatically Build Knowns Database

Value Matching for Data Frames

Combine Two Objects

combine.TRAMPsamples

Combine TRAMPsamples Objects

create.diffsmatrix

Calculate Matrix of Distances between Peaks

demo.knowns

Demonstration Knowns Database

demo.samples

Demonstration Samples Database

group.knowns

Knowns Clustering

Load ABI Output Files

Plot a TRAMP Object

plot.TRAMPknowns

Summary Plot of Knowns Data

plot.TRAMPsamples

Plot a TRAMPsamples Object

Read ABI Output Files

Read/Write TRAMPknowns and TRAMPsamples Objects

rebuild.TRAMP

Rebuild a TRAMP Object

remove.TRAMP.match

Mark a TRAMP Match as Ignored

summary.TRAMP

Create Presence/Absence Matrices from TRAMP Objects

update.TRAMP

Interactively Alter a TRAMP Object

TRAMPR

'TRFLP' Analysis and Matching Package for R

v1.0-10

GPL-2

Authors

Rich FitzJohn [aut, cre], Ian Dickie [aut]

Initial release

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