Plot Transcriptome Index using bootstrapping and confidence intervals

Function to plot and compare the confidence intervals of Transcriptome Index between transformed and non-transformed expression data by using bootstrapping appraoches instead of permutation tests used in PlotSignature.

Usage

PlotCIRatio(ExpressionSet, measure, nbootstraps)

Arguments

ExpressionSet: a standard PhyloExpressionSet, DivergenceExpressionSet or PolymorphismsExpressionSet object.
measure: type of transcriptome index that shall be computed. E.g. measure = "TAI" (Transcriptome Age Index), measure = "TDI" (Transcriptome Divergence Index), measure = "TPI" (Transcriptome Polymorphism Index).
nbootstraps: number of independent bootstraps.

Details

This function can be used to check potential outliers (e.g. a few exramly highly expressed genes) in transcriptome. Since Transcriptome Index is weigthed mean, it could be easily affectd by outliers. So, we have to check potential outliers in the transcriptome data. Because log or sqrt trandformation can alleviate the effect of outliers, if there are some outliers, we could see the confidence intervals (genetated by bootstrapping) from non-trandformed expression data are much higher and more variable than from log or sqrt trandformed expression data. In order to compare the range of confidence intervals in the same scale, we plotted the ratio of upper to lower confidence interval boundary across development.

Author

Jialin Liu

Examples

data("PhyloExpressionSetExample")
PlotCIRatio(PhyloExpressionSetExample,"TAI",5)