Remove bands below LOD

Share:

Description

Function to exclude bands below a given LOD.

Usage

1
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 Fabienne.Flessa@uni-bayreuth.de,
Alexandra Kehl Alexandra.Kehl@botgarten.uni-tuebingen.de,
Matthias Kohl Matthias.Kohl@stamats.de

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

1
2
3
4
5
6
7
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")