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ORCME (version 2.0.2)

monotoneDirection: 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.

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

ORCME, plotIsomeans

Examples

Run this code
  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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