statSights: Statistical methods

In eg-r/sights: Statistics and dIagnostic Graphs for HTS

Statistical methods

Description

Apply any of the available SIGHTS statistical methods

Usage

statSights(statMethod, normMatrix, repIndex, normRows = NULL,
  normCols = NULL, ctrlMethod = NULL, testSide = "two.sided",
  trueMean = 0, ...)

Arguments

statMethod	Statistical testing method to use either 'T' or 'RVM'.
normMatrix	Data frame or numeric matrix of normalized data. Columns are plates, and rows are plate wells.
repIndex	Integer vector indicating replicates in normMatrix. Which plates are replicates of each other? Provide the same number for plates belonging to a replicate group. Each index in the vector matches the corresponding column of normMatrix.
normRows, normCols	Optional integer vector. Indicate which row/column numbers from the normMatrix should be tested. If NULL then all rows/columns from the normMatrix are used.
ctrlMethod	Optional. FDR method to use either 'smoother' or 'bootstrap' to estimate null. Default is NULL, which does not apply FDR control to the statistical testing output.
testSide	Optional. Type of t-test: 'two.sided', 'less', or 'greater'. Default is 'two.sided'.
trueMean	Optional. Number indicating true value of mean. Applies to statMethod 'T'. Default is 0.
...	Optional. Additional parameters passed to qvalue function.

Details

One of the two SIGHTS statistical testing methods may be chosen: statT or statRVM, and FDR control may be applied by statFDR. See their individual help pages for more details.

Value

A matrix of parameters for each replicate group including p-values and q-values, if FDR control is applied.

References

Murie et al. (2015). Improving detection of rare biological events in high-throughput screens. Journal of Biomolecular Screening, 20(2), 230-241.

See Also

Other SIGHTS functions: normSights, plotSights

Examples

## load dataset
data(ex_dataMatrix)

## normalize data matrix using any method and store in new variable
ex_normMatrix <- normSights(normMethod = 'RobZ', dataMatrix = ex_dataMatrix,
dataCols = 5:10, wellCorrection = TRUE)
## choose a statistical testing method, indicate FDR control
## and provide relevant information
ex_statMatrix <- statSights(normMatrix = ex_normMatrix, statMethod = 'RVM',
ctrlMethod = 'smoother', repIndex = c(1,1,1,2,2,2))

eg-r/sights documentation built on Jan. 28, 2023, 12:17 a.m.