relAbForTimes: Relative Abundance from Counts, for multiple time points
In HegemanLab/ProteinTurnover: Protein Turnover Experiment Analysis

Description Usage Arguments Details Value See Also Examples

Gets relative abundance of each channel from counts taken at several retention times, and over multiple time points

relAbForTimes(Count, Channel, RT, TimePoint, data, nboot = 0, ...)

regressionPlot(x, ...)

## S3 method for class 'RelAbTimes'
plot(x, ..., type = c("relAb", "regression"))

makeRelAb(seq, regression.model, nboot = 0)

`Count`	Observed counts
`Channel`	Channels corresponding to the observed counts
`RT`	Retention times corresponding to the observed counts
`TimePoint`	Time points corresponding to the observed counts
`data`	An optional data frame to take the preceding variables from
`nboot`	Experimental, for bootstrapping
`...`	Additional parameters to be passed
`x`	A regRelAbTimes or logRelAbTimes object to be plotted
`type`	desired type of plot
`seq`	the sequence to get the relative abundance for
`regression.model`	passed as method to relAbFromCounts

The data from each time point is fit separately, using relAbFromCounts. Plots are created using the lattice library.

A list is returned with the following elements. It is of class "regRelAbTimes" if a regression method is used and "logRelAbtimes" if a log model is used.

`data.long`	The long data frames from each fit, bound together into one data frame.
`norm_channel`	The chosen baseline channel for each timepoint
`coefs`	For the regression model, a list with the fitted coefficients at each time points.
`relab`	The fitted relative abundance at each channel and timepoint
`proportion`	The fitted relative abundance, converted to a proportion
`method`	The method used
`threshold`	The threshold used