target_quant {dPCP} | R Documentation |
Calculation of targets concentration.
Description
This function calculates the concentration of the targets according to the Poisson distribution.
Usage
target_quant(data.cluster, sample.table)
Arguments
data.cluster |
an object of class |
sample.table |
object of class |
Value
An object of class target_quant
containing a sublist for
each sample. Each sublist has the following components:
quality |
quality threshold used in |
reference |
reference ID. |
raw results |
a data frame with the results of the quantification. |
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)
[Package dPCP version 2.0.1 Index]