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ACGHnorm

Normalizes two channel array CGH data with LOESS, median or mode. If median or mode normalization is used, missing values are imputed. Cellular admixture correction of tumor samples has been deprecated.

The component outputs the residuals of the fit (i.e., normalized case channel), the fit curve, and the unchanged control channel. The latter is included to simplify code downstream from ACGHnorm.

Version 1.4
Bundle microarray
Categories Normalization Preprocessing Copy Number Analysis
Authors Riku Louhimo (Riku.Louhimo@Helsinki.FI)
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Requires R ; limma (R-bioconductor) ; CGHcall (R-bioconductor)
Source files component.xml ACGHnorm.r
Usage Example with default values

Inputs

Name Type Mandatory Description
caseIn CSV Mandatory Probe intensities of the case channel of an Array CGH experiment, preferrably as output by AgilentReader.
control CSV Mandatory Probe intensities of the control channel of an Array CGH experiment, preferrably as output by AgilentReader.
admixtureMatrix CSV Optional Two column csv containing sample names as first column and the proportion of tumor versus normal cells (i.e., samplewise cell admixture) as the second column. Only used if 'adjustCellularity=true'. Deprecated.
probeAnnotation CSV Optional Optional annotation table for expression probes. Must contain columns for 'probeid', 'chr','start' and 'end' the exact values of which are given as parameters.

Outputs

Name Type Description
casechannel LogMatrix Normalized intensities for the case channel (the residuals of the fit).
controlchannel LogMatrix The control channel matrix.
fit LogMatrix The fit curve.

Parameters

Name Type Default Description
adjustCellularity boolean false Adjust for the cellular admixture of each sample (i.e., proportion of cancer versus normal cells in sample). See admixtureMatrix input. This parameter is only used if method is one of 'median' or 'mode'. Deprecated.
chrCol string "Chr" Column name of chromosome annotation. This parameter is only used if method is one of 'median' or 'mode'.
endCol string "End" Column name of probe position end locus. This parameter is only used if method is one of 'median' or 'mode'.
idCol string "" Column name of probe ids. If not given, assumed to be the first column. This parameter is only used if method is one of 'median' or 'mode'.
iterations int 4 Number of iterations of loess fit. Only used if method='loess'.
method string "loess" Normalization method to be used. One of 'loess', 'median' or 'mode'.
span float 0.3 Numeric parameter between 0 and 1 specifying proportion of data to be used in the local regression moving window. Larger numbers give smoother fits. Only used if method='loess'.
startCol string "Start" Column name of probe position start locus. This parameter is only used if method is one of 'median' or 'mode'.

Test cases

Test case Parameters IN
caseIn
IN
control
IN
admixtureMatrix
IN
probeAnnotation
OUT
casechannel
OUT
controlchannel
OUT
fit
case1 (missing) caseIn control (missing) (missing) casechannel controlchannel fit
case2 properties caseIn control (missing) (missing) casechannel (missing) fit

iterations=3,
span=0.5

case3 properties caseIn control admixtureMatrix probeAnnotation casechannel controlchannel (missing)

method = median,
adjustCellularity = true,
idCol = ID,
chrCol = chromosome,
startCol = startLocus,
endCol = endLocus


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