RFLPtools (version 2.0)

RFLPlod: Remove bands below LOD

Description

Function to exclude bands below a given LOD.

Usage

RFLPlod(x, LOD)

Arguments

x

data.frame with RFLP data.

LOD

threshold for low-bp bands.

Value

A data.frame with variables

Sample

character: sample identifier.

Band

integer: band number.

MW

integer: molecular weight.

Gel

character: gel identifier.

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.

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

# NOT RUN {
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")
# }