calcLinear {RPPanalyzer}

Calculates sample concentrations using linear model fit

Description

calculates sample concentrations of a RPPA data set, using parameter of a linear model fitted to the dilution series.

Usage

calcLinear(x, sample.id = c("sample", "sample.n"), dilution = "dilution"
, method = "quantreg", plot = F, detectionLimit = T)

Arguments

x

List containing background corrected RPPA data set

sample.id

character vector refering to column names from which samples can be separated

dilution

column name from the column in feature data that describes the dilution steps of each sample

method

character string describing the method used for the linear fit

plot

logical. If true dilution curves are plotted

detectionLimit

logical. If true model is fitted on dilution steps above the detection limit. If false, all data points are used to fit the model

Value

expression

matrix with protein expression data

dummy

matrix with protein expression data

arraydescription

data frame with feature data

sampledescription

data frame with pheno data

Note

for calculation of serial diluted samples only

Author(s)

Heiko Mannsperger <[e-mail]>,Stephan Gade <[e-mail]>

Examples

## Not run: 
library(RPPanalyzer)
data(ser.dil.samples)

predicted.data <- calcLinear(ser.dil.samples,sample.id=c("sample","sample.n"),
dilution="dilution")

## End(Not run)