tigre-package {tigre} | R Documentation |
This package implements the method of Gao et al. (2008) and Honkela et al. (2010) for Gaussian process modelling single input motif regulatory systems with time-series expression data. The method can be used to rank potential targets of transcription factors based on such data.
Package: | tigre |
Type: | Package |
Version: | 1.12.0 |
Date: | 2012-10-02 |
License: | A-GPL Version 3 |
For details of using the package please refer to the Vignette.
Antti Honkela, Pei Gao, Jonatan Ropponen, Miika-Petteri Matikainen, Magnus Rattray, Neil D. Lawrence
Maintainer: Antti Honkela <antti.honkela@hiit.fi>
A.~Honkela, P.~Gao, J.~Ropponen, M.~Rattray, and N.~D.~Lawrence. tigre: Transcription factor Inference through Gaussian process Reconstruction of Expression for Bioconductor. Bioinformatics 27(7):1026-1027, 2011. DOI: 10.1093/bioinformatics/btr057.
P.~Gao, A.~Honkela, M.~Rattray, and N.~D.~Lawrence. Gaussian process modelling of latent chemical species: applications to inferring transcription factor activities. Bioinformatics 24(16):i70–i75, 2008. DOI: 10.1093/bioinformatics/btn278.
A.~Honkela, C.~Girardot, E.~H. Gustafson, Y.-H. Liu, E.~E.~M. Furlong, N.~D. Lawrence, and M.~Rattray. Model-based method for transcription factor target identification with limited data. Proc Natl Acad Sci USA 107(17):7793-7798, 2010. DOI: 10.1073/pnas.0914285107.
## Not run: # Load a mmgmos preprocessed fragment of the Drosophila developmental # time series data(drosophila_gpsim_fragment) # Get the target probe names library(annotate) aliasMapping <- getAnnMap("ALIAS2PROBE", annotation(drosophila_gpsim_fragment)) twi <- get('twi', env=aliasMapping) fbgnMapping <- getAnnMap("FLYBASE2PROBE", annotation(drosophila_gpsim_fragment)) targetProbe <- get('FBgn0035257', env=fbgnMapping) # Learn the model model <- GPLearn(drosophila_gpsim_fragment, TF=twi, targets=targetProbe, useGpdisim=TRUE, quiet=TRUE) # Plot it GPPlot(model, nameMapping=getAnnMap("FLYBASE", annotation(drosophila_gpsim_fragment))) ## End(Not run)