git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@51844 bc3139a8-67e5-0310-9ffc-ced21a209358
Benilton Carvalho authored on 10/01/2011 12:01:03
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- ************************************************** |
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- * * |
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- * 1.3 SERIES NEWS * |
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- * * |
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- ************************************************** |
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- |
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-USER VISIBLE CHANGES |
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- |
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- o 3 new classes created: |
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- |
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- i. 'ABset': container for quantile-normalized A and B |
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- intensities for both SNP and copy number probes. Required |
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- assay data elements are 'A' and 'B'. Extends eSet |
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- directly. |
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- |
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- - For nonpolymorphic probes, the quantile normalized |
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- intensity is stored in the 'A' assay data element. |
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- The corresponding row in the 'B' assay data element |
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- is NA. This is a bit inefficient, but greatly |
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- simplifies downstream analyses. In particular, '[' |
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- works. |
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- |
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- ii. 'CrlmmSetList': container for results from preprocessing |
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- and genotyping. This object is a list. The first |
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- element of the list is an ABset. The second element is a |
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- SnpSet containing genotype calls. The two elements are |
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- required to have identical featureNames and sampleNames. |
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- |
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- - added several methods for subsetting and accessing |
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- elements of this object, including featureNames, |
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- sampleNames, and "[". |
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- |
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- iii. 'CopyNumberSet': contains locus-level estimates of copy |
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- number for SNPs and polymorphic probes. |
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- |
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- - Required assay data elements are 'CA' and 'CB', |
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- corresponding to the absolute copy number for allele |
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- A and B, respectively. |
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- |
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- - For nonpolymorphic probes, the total copy number is |
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- stored in the 'CA' slot and a NA is recorded for the |
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- corresponding row in the CB matrix. |
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- |
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- - Useful methods: 'copyNumber', 'ellipse', 'points' |
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- |
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- o 'crlmmWrapper' function does preprocessing |
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- (quantile-normalization) and genotyping, saving an object of |
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- class CrlmmSetList for each chromosome |
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- |
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- o 'computeCopynumber' now requires an object of class |
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- 'CrlmmSetList' and returns an object of class 'CopyNumberSet'. |
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@45815 bc3139a8-67e5-0310-9ffc-ced21a209358
Benilton Carvalho authored on 08/04/2010 11:01:11
| 1 | 1 |
new file mode 100644 |
| ... | ... |
@@ -0,0 +1,51 @@ |
| 1 |
+ ************************************************** |
|
| 2 |
+ * * |
|
| 3 |
+ * 1.3 SERIES NEWS * |
|
| 4 |
+ * * |
|
| 5 |
+ ************************************************** |
|
| 6 |
+ |
|
| 7 |
+USER VISIBLE CHANGES |
|
| 8 |
+ |
|
| 9 |
+ o 3 new classes created: |
|
| 10 |
+ |
|
| 11 |
+ i. 'ABset': container for quantile-normalized A and B |
|
| 12 |
+ intensities for both SNP and copy number probes. Required |
|
| 13 |
+ assay data elements are 'A' and 'B'. Extends eSet |
|
| 14 |
+ directly. |
|
| 15 |
+ |
|
| 16 |
+ - For nonpolymorphic probes, the quantile normalized |
|
| 17 |
+ intensity is stored in the 'A' assay data element. |
|
| 18 |
+ The corresponding row in the 'B' assay data element |
|
| 19 |
+ is NA. This is a bit inefficient, but greatly |
|
| 20 |
+ simplifies downstream analyses. In particular, '[' |
|
| 21 |
+ works. |
|
| 22 |
+ |
|
| 23 |
+ ii. 'CrlmmSetList': container for results from preprocessing |
|
| 24 |
+ and genotyping. This object is a list. The first |
|
| 25 |
+ element of the list is an ABset. The second element is a |
|
| 26 |
+ SnpSet containing genotype calls. The two elements are |
|
| 27 |
+ required to have identical featureNames and sampleNames. |
|
| 28 |
+ |
|
| 29 |
+ - added several methods for subsetting and accessing |
|
| 30 |
+ elements of this object, including featureNames, |
|
| 31 |
+ sampleNames, and "[". |
|
| 32 |
+ |
|
| 33 |
+ iii. 'CopyNumberSet': contains locus-level estimates of copy |
|
| 34 |
+ number for SNPs and polymorphic probes. |
|
| 35 |
+ |
|
| 36 |
+ - Required assay data elements are 'CA' and 'CB', |
|
| 37 |
+ corresponding to the absolute copy number for allele |
|
| 38 |
+ A and B, respectively. |
|
| 39 |
+ |
|
| 40 |
+ - For nonpolymorphic probes, the total copy number is |
|
| 41 |
+ stored in the 'CA' slot and a NA is recorded for the |
|
| 42 |
+ corresponding row in the CB matrix. |
|
| 43 |
+ |
|
| 44 |
+ - Useful methods: 'copyNumber', 'ellipse', 'points' |
|
| 45 |
+ |
|
| 46 |
+ o 'crlmmWrapper' function does preprocessing |
|
| 47 |
+ (quantile-normalization) and genotyping, saving an object of |
|
| 48 |
+ class CrlmmSetList for each chromosome |
|
| 49 |
+ |
|
| 50 |
+ o 'computeCopynumber' now requires an object of class |
|
| 51 |
+ 'CrlmmSetList' and returns an object of class 'CopyNumberSet'. |