relAbFromCounts: Relative Abundance from Counts

In HegemanLab/ProteinTurnover: Protein Turnover Experiment Analysis

Description

Gets relative abundance of each channel from counts taken at several retention times

Usage

relAbFromCounts(Count, Channel, RT, data, TimePoint, method = c("lm", "rlm",
  "lqs", "rq", "sum", "log"), norm_channel, threshold, cutoff, nboot = 0)

Arguments

Count	Observed counts
Channel	Channels corresponding to the observed counts
RT	Retention times corresponding to the observed counts
data	An optional data frame to take the preceding variables from.
TimePoint	The time point that this data is from, to be optionally added to the output data frames.
method	Options are "lm", "rlm", "lqs", "rq", "sum", and "log".
norm_channel	The channel to use as baseline for the regression methods, in the output of the relative abundance, and when computing the threshold. By default, the channel with the highest total counts is used.
threshold	A proportion used to remove values corresponding to retention times for which the value of the norm_channel is less than this threshold times the max of the norm_channel.
cutoff	All counts less than or equal to this are set to missing.
nboot	Experimental, for bootstrapping

Details

The "lm", "rlm", "lqs", and "rq" methods plots the counts for each channel against the baseline channel and computes a regression; the slope is the relative abundance.

The "sum" method simply adds the counts and gets the proportion in each channel.

The "log" method takes the logs of the counts and computes a two-way ANOVA on RT and Channel; the coefficients for the channels are then converted back to relative abundances.

Plots are created using the lattice library.

Value

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

data.wide	A table of counts, by Channel, and RT
data.long	The counts in long data frame format
data	The fitted relative abundance and proportions at each channel.
norm_channel	The chosen baseline channel
coefs	For the regression model, the fitted coefficients
method	The method used
threshold	The threshold used

Examples

data(isocounts)

HegemanLab/ProteinTurnover documentation built on May 6, 2019, 11:50 p.m.