RISAtab: Example of RISA output table from the prepRISA package

In prepRISA: prepRISA

Description

Example of RISA output table from the prepRISA package.

Usage

data(RISAtab)

Format

RISAtab is a data frame with 32 rows and 256 columns. The 32 rows are 32 RISA profiles, comprising 20 standard samples and 12 real soil samples. The 256 columns correspond to the RISA bands detected in the RISA raw profiles by the prepRISA package. The corresponding RISA raw data are in the RISAdata.txt file (3424 rows, 4 columns) located in the prepRISA package directory.

Use system.file("RISAdata.txt", package="prepRISA") to get the exact location of this file on your system.

References

Ranjard L., Nazaret S., Gourbiere F., Thioulouse J., Linet P. & Richaume A. (2000) A soil microscale study to reveal the heterogeneity of Hg(II) impact on indigenous bacteria by quantification of adapted phenotypes and analysis of community DNA fingerprints. FEMS Microbiology Ecology, 31, 107-115.

Ranjard L., Poly F., Combrisson J., Richaume A., Gourbiere F., Thioulouse J. & Nazaret S. (2000) Heterogeneous Cell Density and Genetic Structure of Bacterial Pools Associated with Various Soil Microenvironments as Determined by Enumeration and DNA Fingerprinting Approach (RISA). Microbial Ecology, 39, 263-272.

Ranjard L., Poly F., Lata J.C., Mougel C., Thioulouse J. & Nazaret S. (2001) Characterisation of bacterial and fungal soil communities by automated-RISA (Ribosomal Intergenic Spacer Analysis) fingerprints: biological and methodological variability. Applied and Environmental Microbiology, 67, 4479-4487.

Examples

## Not run: 
data(RISAtab)
library(ade4)
RISApca <- dudi.pca(RISAtab)
s.label(RISApca$li)

## End(Not run)

prepRISA documentation built on May 2, 2019, 6:34 p.m.