statSights: Statistical methods
In sights: Statistics and dIagnostic Graphs for HTS

Description Usage Arguments Details Value References See Also Examples

Apply any of the available SIGHTS statistical methods

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

`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.

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.

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

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

Other SIGHTS functions: normSights, plotSights

## 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))