Up: Component summary
Up: Component summary
Component
SNPArrayReaderImports genotype data from Illumina SNP and Affymetrix SNP 6.0 or 5.0 files.
| Version | 1.7 |
|---|---|
| Bundle | microarray |
| Categories | Data Import Affy Illumina SNP |
| Authors | Riku Louhimo (Riku.Louhimo@Helsinki.FI) |
| Issue tracker | View/Report issues |
| Requires | R ; crlmm (R-bioconductor) ; genomewidesnp5Crlmm (R-package) ; genomewidesnp6Crlmm (R-package) ; human370v1cCrlmm (R-package) ; ff (R-package) |
| Source files | component.xml SNPArrayReader.r |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| dataDir | BinaryFolder | Mandatory | Input file directory. |
| sampleNames | CSV | Mandatory | This file should contain the wanted names for the samples. |
Outputs| Name | Type | Description |
|---|---|---|
| genotypeMatrix | SNPMatrix | Matrix containing the markers as columns and the samples as rows. |
| markerNames | IDList | List containing the markernames. |
| copynumberMatrix | LogMatrix | Matrix containing normalized locus specific logarithmic copy number intensities. |
| probeAnnotation | CSV | Annotations for markers. |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| S2NoiseLimit | int | 5 | Samples with lower Signal-to-Noise ratio are dropped. |
| confLimit | float | 0.95 | Markers with a lower confidence value are set NA. |
| fileCol | string | "" | Column in sampleNames for file names. Default is the first column. See also the sampleCol parameter. |
| fileType | string | (no default) | Set the type of input files. Valid values are 'I' for Illumina data and 'A' for Affymetrix data. |
| getCopyNumbers | boolean | false | Call copy numbers from copy number proces on AffyMetrix arrays. |
| illuminaCDF | string | "human370v1c" | Illumina chip manifest, one of 'human370v1c', 'human550v3b', 'human650v3a', 'human1mv1c', 'human660quadv1a', 'human1mduov3b', 'humanomni1quadv1b', 'humanomniexpress12v1b', 'human370quadv3c', 'human610quadv1b'. |
| sampleCol | string | "" | Column in sampleNames for sample (human readable) names. Default is the first column. See also the fileCol parameter. |
| useAffy5 | boolean | false | Set this to true if input datatype is Affy SNP 5.0. Ignored if fileType='I'. |
| useSymbols | boolean | true | Set the form of the output genotypes. If true then mock genotypes 'AA', 'AB' and 'BB' are used. If false, pseudo-real genotypes 'AA', 'AT' and 'TT' are used. |
Test cases| Test case | Parameters▼ | IN dataDir |
IN sampleNames |
OUT genotypeMatrix |
OUT markerNames |
OUT copynumberMatrix |
OUT probeAnnotation |
|---|---|---|---|---|---|---|---|
| case1 | properties | dataDir | sampleNames | (missing) | (missing) | (missing) | (missing) |
|
fileType = A, |
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| case2 | properties | dataDir | sampleNames | (missing) | (missing) | (missing) | (missing) |
|
S2NoiseLimit = 0, |
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| case3 | properties | dataDir | sampleNames | (missing) | (missing) | (missing) | (missing) |
|
fileType = I, |
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