AssayCorrector (version 2.0.0)

create_assay: Create a new assay

Description

create_assay makes a new object of class assay. You should pass this object to detect_bias() and correct_bias() methods

Usage

create_assay(m, ctrl = NA)

Arguments

m

The assay you want to be corrected

ctrl

An optional boolean array of the same dimensions as m. Each entry is 1 if the well is a control well, 0 otherwise. All control wells are excluded from all computations

Value

assay The created assay object. It containts the following fields:

n The HTS matrix of raw measurements

ctrl The binary matrix of control wells

biasPositions The binary matrix where 1:well is biased, 0:well is unbiased, as suggested by Mann-Whitney test

mCorrected The HTS matrix of corrected measurements, initilized to a zero array, and subsequently storing the corrected version of m via correct_bias()

biasType Vector of length p, where p is the number of plates. It tells, for each plate of the assay, A:Additive trend, M:Multiplicative trend, U:Undetermined trend and C:Error-free plate.

biasModel Vector of length p, where p is the number of plates. It tells, for each plate of the assay, the most likely spatial bias model (1 through 6)

biasConf Vector of length p, where p is the number of plates. It tells, for each plate of the assay, the confidence in the model, (0 - lowest to 3- highest). It is computed by counting the number of bias models (additive or mutliplicative) which agree together.

Examples

# NOT RUN {
# Fictive 8x12x5 assay
assay<-create_assay(m)
# Plate 7 taken from Carralot et al. 2012
assay<-create_assay(plate7)
# }