readSummaries: Read summaries generated by crlmm
In jmacdon/oligo: Preprocessing tools for oligonucleotide arrays
Description
Usage
Arguments
Details
Value
Description
This function read the different summaries generated by crlmm.
Usage
1
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.
jmacdon/oligo documentation built on Aug. 11, 2020, 12:32 a.m.
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Description Usage Arguments Details Value
Description
This function read the different summaries generated by crlmm.
Usage
1 | readSummaries(type, tmpdir)
|
Arguments
type |
type of summary of |
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.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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