Description Usage Arguments Value Examples
For each pipeline, differential expression is estimated by fold change on mean signals across replicates of cell lines. For features that are truely differential expressed, their fold changes levels are summarized based on different levels of detrended logsignals.
1 2 
dat 
A 
positive 
A logical vector with length equivalent to row
number of matrices in 
fcsign 
A numeric vector with length equivalent to row
number of matrices in 
constant 
A numeric constant that is added to quantifications before fold changes calculation. (default: 0.5) 
loessspan 
A numeric number indicating span used
for loess smooth. Details see

thresholds 
A numeric vector defining cutoffs on fold changes as the points to make threshold averaging on ROC curves. (default: seq(12, 0, len = 300)) 
... 
Parameters for base function 
plot 
Fold change plots for all the quantification pipelines. 
list 
A list of two numeric vectors indicating median and standard error of fold changes in three different levels of detrended logsignals. 
1 2 3 4 5 6 7 8 9 10 11  data(simdata)
condInfo < factor(simdata$samp$condition)
repInfo < factor(simdata$samp$replicate)
evaluationFeature < rep(TRUE, nrow(simdata$meta))
calibrationFeature < simdata$meta$house & simdata$meta$chr == 'chr1'
unitReference < 1
dat < signalCalibrate(simdata$quant, condInfo, repInfo, evaluationFeature,
calibrationFeature, unitReference, calibrationFeature2 = calibrationFeature)
## only select the true differential that have exact fold changes
simdata$meta$fcsign[simdata$meta$fcstatus == "off.on"] < NA
plotFC(dat,simdata$meta$positive,simdata$meta$fcsign)

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