Description Usage Details Value Author(s) References See Also Examples
prepRISA is a package to read RISA data coming from a sequencer and compile them into a dataframe that is suitable for multivariate data analysis.
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This function will interactively ask for a variable number of
parameters. It reads a RISA file that comes from a sequencer
(text file with 4 columns: 1=sample name, 2=peak number, 3=peak
position (number of base pairs), 4=peak height). The data are treated
according to the parameters given by the user, and a samples x peaks
table is computed. This table can then be analysed with the ade4
package. Two text files are written to disk : one with all columns and
one where columns of zeroes are removed.
prepRISA.CLI
uses the CLI (command line interface) to dialog
with the user, while prepRISA.GUI
uses a Tk GUI (graphical user
interface). Both interfaces call the same function prepRISAfun
.
For efficiency reasons, computations are done in a C function called
repClass
.
The prepRISA.CLI
function returns invisibly the samples x peaks
table as a dataframe,
so that it can be used subsequently in ade4 like this:
tab <- prepRISA.CLI()
...
pca1 <- dudi.pca(tab)
Note that these tables can be quite large (hundreds of columns).
The prepRISA.GUI
returns nothing, as the output dataframe is directly affected in the function:
prepRISA.GUI()
...
pca1 <- dudi.pca(tab)
Jean Thioulouse jean.thioulouse at univ-lyon1.fr
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.
RISAtab
for an example of RISA data.
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tab <- prepRISA()
## End(Not run)
|
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