statSights {sights} | R Documentation

## 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))

[Package sights version 1.20.0 Index]