RPPanalyzer (version 1.3)

calcLinear: 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

Examples

library(RPPanalyzer)
data(ser.dil.samples)

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