RFLPlod: Remove bands below LOD

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/RFLPlod.R

Description

Function to exclude bands below a given LOD.

Usage

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RFLPlod(x, LOD)

Arguments

x

data.frame with RFLP data.

LOD

threshold for low-bp bands.

Details

Low-bp bands may be regarded as unreliable. Function RFLPlod can be used to exclude such bands, which are likely to be absent in some other samples, before further analyses.

Value

A data.frame with variables

Sample

character: sample identifier.

Band

integer: band number.

MW

integer: molecular weight.

Gel

character: gel identifier.

Author(s)

Fabienne Flessa [email protected],
Alexandra Kehl [email protected],
Matthias Kohl [email protected]

References

Flessa, F., Kehl, A., Kohl, M. Analysing diversity and community structures using PCR-RFLP: a new software application. Molecular Ecology Resources 2013 Jul; 13(4):726-33.

See Also

RFLPdata

Examples

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data(RFLPdata)
## remove bands with MW smaller than 60
RFLPdata.lod <- RFLPlod(RFLPdata, LOD = 60)
par(mfrow = c(1, 2))
RFLPplot(RFLPdata, nrBands = 4, ylim = c(40, 670))
RFLPplot(RFLPdata.lod, nrBands = 4, ylim = c(40, 670))
title(sub = "After applying RFLPlod")

RFLPtools documentation built on May 30, 2017, 2:09 a.m.