Description Usage Arguments Value Author(s) References See Also Examples
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.
1 |
geneData |
gene expression matrix for all genes |
doseData |
indicates the dose levels |
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. |
Adetayo Kasim, Martin Otava and Tobias Verbeke
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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | 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)
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