getA {oligoClasses} | R Documentation

## Compute average log-intensities / log-ratios

### Description

Methods to compute average log-intensities and log-ratios across alleles, within strand.

### Usage

    getA(object)
    getM(object)
    A(object, ...)
    B(object, ...)

### Arguments

`object` | `SnpQSet`, `SnpCnvQSet` or `TilingFeatureSet2` object.

`...` | arguments to be passed to `allele` - 'sense' and 'antisense' are valid values if the array is pre-SNP_5.0

### Details

For SNP data, SNPRMA summarizes the SNP information into 4 quantities (log2-scale):

- antisenseThetaAantisense allele A. (Not applicable for Affymetrix 5.0 and 6.0 platforms.)

- antisenseThetaBantisense allele B. (Not applicable for Affymetrix 5.0 and 6.0 platforms.)

- senseThetaAsense allele A. (Not applicable for Affymetrix 5.0 and 6.0 platforms.)

- senseThataBsense allele B. (Not applicable for Affymetrix 5.0 and 6.0 platforms.)

- alleleAAffymetrix 5.0 and 6.0 platforms

- alleleBAffymetrix 5.0 and 6.0 platforms

The average log-intensities are given by: `(antisenseThetaA+antisenseThetaB)/2` and `(senseThetaA+senseThetaB)/2`.

The average log-ratios are given by: `antisenseThetaA-antisenseThetaB` and `senseThetaA-senseThetaB`.

For Tiling data, `getM` and `getA` return the log-ratio and average log-intensities computed across channels: `M = log2(channel1)-log2(channel2)` `A = (log2(channel1)+log2(channel2))/2`

When large data support is enabled with the ff package, the AssayData elements of an `AlleleSet` object can be `ff_matrix` or `ffdf`, in which case pointers to the ff object are stored in the assay data. The functions `open` and `close` can be used to open or close the connection, respectively.

### Value

A 3-dimensional array (SNP's x Samples x Strand) with the requested measure, when the input SNP data (50K, 250K).

A 2-dimensional array (SNP's x Samples), when the input is from SNP 5.0 and SNP 6.0 arrays.

A 2-dimensional array if the input is from Tiling arrays.

### See Also

`snprma`

[Package oligoClasses version 1.48.0 Index]