lmms (version 1.3.3)

plot.noise: Plot of associations objects

Description

Plot of the filter ratios R_T and R_I as proposed by Straube et al 2014.

Usage

"plot"(x, colorBy = "propMissing", fcCutoff = NA, propMissingCutoff = NA, ...)

Arguments

x

an object of class matrix or data.frame.

colorBy

associations the variable to be colored by. Default 'propMissing', options: 'propMissing','fc'.

fcCutoff

an optional numeric value to remove ratios with low fold changes.

propMissingCutoff

an optional numeric value to remove ratios with high number of missing values.

...

ignored

Value

plot showing filter ratios R_T and R_I as proposed by Straube et al. 2014. Filter ratios can either be colored by proportion of missing values or maximum fold change.

References

Straube J., Gorse D., Huang B.E., Le Cao K.-A.(2014). A linear mixed model spline framework for analyzing time course 'omics' data Submitted

See Also

investNoise, filterNoise

Examples

## Not run: 
# data(kidneySimTimeGroup)
# G1 <- kidneySimTimeGroup$group=="G1"
# noiseTest <-investNoise(data=kidneySimTimeGroup$data[G1,],time=kidneySimTimeGroup$time[G1],
#             sampleID=kidneySimTimeGroup$sampleID[G1])
# plot(noiseTest,colorBy="fc")
# ## End(Not run)