create_assay: Create a new 'assay'

In AssayCorrector: Detection and Correction of Spatial Bias in HTS Screens

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

# Fictive 8x12x5 assay
assay<-create_assay(m)
# Plate 7 taken from Carralot et al. 2012
assay<-create_assay(plate7)

Example output

Loading required package: RColorBrewer
Loading required package: lattice
Loading required package: latticeExtra
Loading required package: kSamples
Loading required package: SuppDists
Loading required package: RVAideMemoire
*** Package RVAideMemoire v 0.9-73 ***

AssayCorrector documentation built on May 2, 2019, 6:59 a.m.