monotoneDirection {ORCME} | R Documentation |
The monotone means under increasing/decreasing trend
Description
The function calculates the likelihood for the increasing and decreasing trend in the dose response for all the given genes separately gene-by-gene. The trend with the higher likelihood is chosen and the isotonic regression is applied on the means.
Usage
monotoneDirection(geneData, doseData)
Arguments
geneData |
gene expression matrix for all genes |
doseData |
indicates the dose levels |
Value
A list with components
direction |
the direction with the higher likelihood of increasing (indicated by "up") or decreasing (indicated by "dn") trend. |
incData |
isotonic means with respect to dose for those genes that were classified as following the increasing trend. |
decData |
isotonic means with respect to dose for those genes that were classified as following the decreasing trend. |
obsincData |
observed gene expression matrix for those genes that were classified as following the increasing trend. |
obsdecData |
observed gene expression matrix for those genes that were classified as following the decreasing trend. |
arrayMean |
isotonic means with respect to dose for all genes. |
Author(s)
Adetayo Kasim, Martin Otava and Tobias Verbeke
References
Lin D., Shkedy Z., Yekutieli D., Amaratunga D., and Bijnens, L. (editors). (2012) Modeling Dose-response Microarray Data in Early Drug Development Experiments Using R. Springer.
Cheng, Y. and Church, G. M. (2000). Biclustering of expression data. In: Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology, 1, 93-103.
See Also
Examples
data(doseData)
data(geneData)
dirData <- monotoneDirection(geneData = geneData,doseData = doseData)
## direction of monotone trend
Direction <- dirData$direction
## Isotonic means for upward genes
incData <- as.data.frame(dirData$incData)
##Isotonic means for downward genes
decData <- as.data.frame(dirData$decData)
## observd data upward genes
obsIncData <- as.data.frame(dirData$obsincData)
## observed data for downward genes
obsDecData <- as.data.frame(dirData$obsdecData)
## isotonic means for all genes
isoMeans <- as.data.frame(dirData$arrayMean)