replicates_quant {dPCP}

Calculation of targets concentration, pooling the sample replicates

Description

This function calculates the concentration of the targets, combining the results of the replicates of each sample.

Usage

replicates_quant(raw.results, sample.table)

Arguments

raw.results

an object of class target_quant, inherited from target_quant.

sample.table

object of class sample_table, inherited from read_sampleTable.

Value

An object of class replicates_quant containing a sublist for every sample. Each sublist has the following components:

quality

quality threshold used in read_sample.

reference

reference ID.

raw results

a data frame with the results of quantification.

replicates results

a data frame with the results of quantification of pooled replicates.

Examples

library(dPCP)

#Find path of sample table and location of reference and input files
sampleTable <- system.file("extdata", "Template_sampleTable.csv",
                     package = "dPCP")

fileLoc <- system.file("extdata", package = "dPCP")

#Read sample table file
sample.table <- read_sampleTable(sampleTable, system = "bio-rad",
                                 file.location = fileLoc)

#Read reference files
ref <- read_reference(sample.table, system = "bio-rad",
                      file.location = fileLoc)

#Read samples files
samp <- read_sample(sample.table, system = "bio-rad",
                   file.location = fileLoc)

#Reference DBSCAN clustering
dbref <- reference_dbscan(ref, sample.table, save.template = FALSE)

#Predict position of clusters centroid from reference DBSCAN results
cent <- centers_data(samp, sample.table,dbref)

#Fuzzy c-means clustering
cmclus <- cmeans_clus(cent)

#Rain classification.
rainclus <- rain_reclus(cmclus)

#Quantification
quantcm <- target_quant(cmclus, sample.table)
quant <- target_quant(rainclus, sample.table)

#Replicates pooling
rep.quant <- replicates_quant(quant, sample.table)