filterArray {MmPalateMiRNA} | R Documentation

## Filter an `RGList` object to remove probes

### Description

Filters an `RGList` object to remove probes with foreground intensities not sufficiently above the background intensity. Additionally can filter probes based on character strings, to remove e.g. control probes.

### Usage

    filterArray (obj, ...)
    ## S4 method for signature 'RGList'
    filterArray(obj, keep, frac, number, reps)

### Arguments

`obj` | An `RGList` object
`keep` | Character vector to be used as a text filter. Only gene names (as contained in `obj$genes$Name`) which contain these text strings will be retained.
`frac` | Fraction to use as a background filter. Only those probes with foreground values (both red and green) greater than 'frac' times the background values pass the filter.
`number` | The number of samples required to pass the background filter for each probe.
`reps` | The number of replicates for each probe required to pass the filtering step.
`...` | allows additional arguments to be passed to specific methods

### Value

Returns an `RGList` object identical in structure to the input object, but with reduced dimension according to the filtering steps.

### Methods

`signature(obj = "RGList")`

### See Also

`checkMVs`, `fixMVs`, `checkOutliers`, `fixOutliers`

### Examples

    data(PalateData)
    reducedSet <- filterArray(PalateData, keep=c("MIR", "LET", "POSCON", "CALIB"),
                              frac=1.1, number=3, reps=4)

[Package MmPalateMiRNA version 1.30.0 Index]