create_dpcr: Create dpcR object

In dpcR: Digital PCR Analysis

Description

Creates adpcr and dpcr objects from data.

Usage

create_dpcr(data, n, exper = "Experiment 1", replicate = NULL,
  assay = "Unknown", type, v = 1, uv = 0, threshold = 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).
v	The volume of partitions [nL].
uv	The volume uncertainty of partitions [nl].
threshold	numeric value giving the threshold above which droplet is counted as positive. Ignored if adpcr is TRUE.
adpcr	logical. If TRUE, function creates adpcr object. If FALSE, function creates dpcr 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.

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.

Value

An adpcr or dpcr object.

Note

create_dpcr is a preferred to calling directly new.

Currently only end-point measurements are supported.

Author(s)

Michal Burdukiewicz, Stefan Roediger.

See Also

Streamlined, but more limited version: df2dpcr

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)

dpcR documentation built on May 2, 2019, 7:04 a.m.