calcLinear {RPPanalyzer}R Documentation

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
expression_b 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 <h.mannsperger@dkfz.de>,Stephan Gade <s.gade@dkfz.de>

Examples


library(RPPanalyzer)
data(subsetdataI)

datalinear <- calcLinear(subsetdataI,sample.id=c("sample","sample.n")
                           ,dilution="dilution")

[Package RPPanalyzer version 1.0.2 Index]