readSummaries {oligo} | R Documentation

## Read summaries generated by crlmm

### Description

This function read the different summaries generated by crlmm.

### Usage

    readSummaries(type, tmpdir)

### Arguments

`type` | type of summary of `character` class: 'alleleA', 'alleleB', 'alleleA-sense', 'alleleA-antisense', 'alleleB-sense', 'alleleB-antisense', 'calls', 'llr', 'conf'.
`tmpdir` | directory containing the output saved by crlmm

### Details

On the 50K and 250K arrays, given a SNP, there are probes on both strands (sense and antisense). For this reason, the options 'alleleA-sense', 'alleleA-antisense', 'alleleB-sense' and 'alleleB-antisense' should be used **only** with such arrays (XBA, HIND, NSP or STY).

On the SNP 5.0 and SNP 6.0 platforms, this distinction does not exist in terms of algorithm (note that the actual strand could be queried from the annotation package). For these arrays, options 'alleleA', 'alleleB' are the ones to be used.

The options `calls`, `llr` and `conf` will return, respectivelly, the CRLMM calls, log-likelihood ratios (for devel purpose **only**) and CRLMM confidence calls matrices.

### Value

Matrix with values of summaries.

[Package oligo version 1.44.0 Index]