dpcR (version 0.3)

create_dpcr: Create dpcR object

Description

Creates adpcr and ddpcr objects from data.

Usage

create_dpcr(data, n, exper = "Experiment 1", replicate = NULL, assay = "Unknown", type, threshold = NULL, breaks = NULL, adpcr, col_names = NULL, row_names = NULL, panel_id = NULL)

Arguments

data

a numeric vector or matrix of data from dPCR experiments. Data frames will be converted to matrices.

n

integer equal to number of partitions.

exper

The id of experiments.

replicate

The id of technical replicates.

assay

The name or id of assays.

type

Object of class "character" defining type of data. Could be "nm" (number of molecules per partition), "tnp" (total number of positive wells in the panel), "fluo" (fluorescence), "np" (status (positive (1) or negative(0)) of each droplet) or"ct" (threshold cycle).

threshold

numeric value giving the threshold above which droplet is counted as positive. Ignored if adpcr is TRUE.

breaks

numeric vector giving the number of intervals into which data should be cut. Ignored if adpcr is FALSE.

adpcr

logical. If TRUE, function creates adpcr object. If FALSE, function creates ddpcr object.

col_names

character vector of column names in array. Ignored if not adcpr.

row_names

character vector of row names in array. Ignored if not adcpr.

panel_id

factor vector of panel IDs (or names). Ignored if not adcpr.

Value

An adpcr or ddpcr object.

Details

This constructor function assists in creation of objects used by other functions of the package. It is also responsible for checking the correctness of arguments.

A warning is prompted whenever any of arguments is converted to other type.

Examples

# Droplet digital PCR example
sample_runs <- matrix(rpois(60, lambda = 1.5), ncol = 2)
ddpcr1 <- create_dpcr(sample_runs[,1], n = 30L, 
threshold = 1, type = "nm", adpcr = FALSE)
ddpcr2 <- create_dpcr(sample_runs[,2], n = 30L, 
threshold = 1, type = "nm", adpcr = FALSE)
plot_vic_fam(ddpcr1, ddpcr2)

# Array digital PCR example
sample_adpcr <- create_dpcr(rpois(765, lambda = 0.8), n = 765L, 
			    type = "nm", adpcr = TRUE)
plot_panel(sample_adpcr, 45, 17)