pmm-package: The PMM-Package
In pmm: Parallel Mixed Model

Description Details Author(s) References

This package contains R functions for fitting the Parallel Mixed Model and analyzing its results.

The Parallel Mixed Model (PMM) approach is suitable for hit selection and cross-comparison of RNAi screens generated in experiments that are performed in parallel under several conditions. As an example, we could think of the measurements or readouts from cells under RNAi knock-down, which are infected with several pathogens or which are grown from different cell lines. PMM simultaneously takes into account all the knock-down effects in order to gain statistical power for the hit detection. As a special feature, PMM allows incorporating RNAi weights that can be assigned according to the additional information on the used RNAis or the screening quality.
The following functions are contained in this R-package:

`pmm`	fits the PMM
`hitheatmap`	visualizes the results of PMM
`sharedness`	computes the sharedness

Anna Drewek <adrewek@stat.math.ethz.ch>

Rämö, P., Drewek, A., Arrieumerlou, C., Beerenwinkel, N., Ben-Tekaya H., Cardel, B., Casanova, A., Conde-Alvarez. R., Cossart, P., Csucs, G., Eicher, S., Emmenlauer, M. Greber, U., Hardt, W.-D., Helenius, A., Kasper, C., Kaufmann, A., Kreibich, S., Kuebacher, A., Kunszt, P., Low, S.H., Mercer, J., Mudrak, D., Muntwiler, S., Pelkmans, L., Pizarro-Cerda, J., Podvinec, M., Pujadas, E., Rinn, B., Rouilly, V., Schmich F., Siebourg, J., Snijder, B., Stebler, M., Studer, G., Szczurek, E., Truttmann, M., von Mering, C., Vonderheit, A., Yakimovich, A., Buehlmann, P. and Dehio, C., Simultaneous analysis of large-scale RNAi screens for pathogen entry, BMC Genomics 15(1162): p.1471-2164. (2014)

pmm documentation built on Nov. 8, 2020, 6:55 p.m.