modifyWeights {limma} | R Documentation

## Modify Matrix of Weights By Control Status of Rows

### Description

Modify weights matrix for given gene status values.

### Usage

    modifyWeights(weights=rep(1,length(status)), status, values, multipliers)

### Arguments

`weights` | numeric matrix of relative weights, rows corresponding to genes and columns to arrays
`status` | character vector giving the control status of each spot on the array, of same length as the number of rows of `weights`
`values` | character vector giving subset of the unique values of `status`
`multipliers` | numeric vector of same length as `values` giving factor by which weights will be modified

### Details

The function is usually used to temporarily modify the weights matrix during normalization of data. The function can be used for example to give zero weight to spike-in ratio control spots during normalization.

### Value

Numeric matrix of same dimensions as `weights` with rows corresponding to `values` in `status` modified by the specified multipliers.

### Author(s)

Gordon Smyth

### See Also

An overview of normalization functions available in LIMMA is given in 05.Normalization.

### Examples

    w <- matrix(runif(6*3),6,3)
    status <- c("Gene","Gene","Ratio_Control","Ratio_Control","Gene","Gene")
    modifyWeights(w,status,values="Ratio_Control",multipliers=0)

[Package limma version 3.42.2 Index]