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SNPArrayReader

Imports 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)
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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,
fileCol = filenames,
sampleCol = samplenames

case2 properties dataDir sampleNames (missing) (missing) (missing) (missing)

S2NoiseLimit = 0,
confLimit = 0.9,
useAffy5 = true,
fileType = A

case3 properties dataDir sampleNames (missing) (missing) (missing) (missing)

fileType = I,
S2NoiseLimit = 0


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