oligo (version 1.36.1)

readSummaries: 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

Value

• Matrix with values of summaries.

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.