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CN2GECollection

Encapsulates three algorithms with similar inputs for copy number to RNA expression integration. All inputs must be in the same order and have matching IDs.

In pint (R Bioconductor), canonical correlation analysis using pSimCCA to detect integrative effects of CNA and gene expression. Inputs must be matched i.e., dim(exprMatrix) = dim(cnaMatrix) and rows (samples) and columns (genes/transcripts/exons) match.

In DRI (R CRAN), either a standard correlation coefficient between the two data or a supervised learning method is employed to detect similarily directed abnormalities.

In edira, equally directed deviations from reference samples are detected by combined modified correlation coefficient followed by a Wilcoxon test.

Version 1.0
Bundle microarray
Categories Integration Copy Number Analysis
Authors Riku Louhimo (Riku.Louhimo@Helsinki.FI)
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Requires edira (R-package) ; mixOmics (R-package) ; pint (R-bioconductor) ; PREDA (R-package) ; SIM (R-bioconductor) ; iCluster (R-bioconductor) ; tilingArray (R-bioconductor)
Source files component.xml CN2GECollection.r
Usage Example with default values

Inputs

Name Type Mandatory Description
exprMatrix LogMatrix Mandatory Matrix of expression values.
cnaMatrix CSV Mandatory Matrix of copy number values.
exprAnnotation AnnotationTable Mandatory Annotations for rows. Shall include id, chromosome and locus.
exprRefMatrix LogMatrix Optional Matrix of normalized expression values from reference samples. Only used if algorithm=edira.
cnaRefMatrix CSV Optional Matrix of normalized copy number values from reference samples. Only used if algorithm=edira.
labels CSV Optional Sample groupings for DRImethod=SAM.

Outputs

Name Type Description
concomitantGenes CSV Genes that show concomitant expression and copy number aberration.
concomitantGenes2 CSV Genes that show concomitant (down) expression and copy number aberration. Output is reserved for SODEGIR output.
plot Latex Clustering plot for iCluster algorithm.

Parameters

Name Type Default Description
DRImethod string "pearson" Specify the integration method for DRI. One of "pearson", "spearman", "ttest" or "SAM", where SAM stands for supervised learing algorithm, and pearson and spearman are variants of the correlation coefficient.
SGRthold float 0.1 Thresholds for test statistic distribution for SODEGIR.
algorithm string (no default) Define the algorithm for integration. Must be one of "pint", "edira", 'SODEGIR', 'SIM', 'iCluster', 'integrOmics' or "DRI".
ediraMaxseg int 50 Maximum number of segments for edira segmentation. Only used if algorithm='edira' and ediraSegment='true'.
ediraSegment boolean false Define whether CNA data is segmentated prior to integration. Only used if algorithm=edira.
endCol string "" Name of the column with probe end locus information.
fdrLimit float 0.1 Result fdr cutoff limit. Only used if algorithm=DRI, SODEGIR or SIM.
iClusterK int 3 Number of K means clusters for iClust.
iClusterOpt boolean false Optimize K for iClust. See 'iClusterK' parameter also. Enabling this slows down processing.
locusCol string "" Name of the column with locus information.
perm int 1000 Number of permutations for null distribution. Only used if algorithm=DRI,SODEGIR.
pintArm string "" Arm for which scores are calculated. Must be one of "p", "q" or empty. Default value indicates both arms to be analyzed. Only used if algorithm=pint.
pintMethod string "pSimCCA" Specify the dependency model: "pCCA" probabilistic canonical correlation analysis (Bach and Jordan 2005) "pPCA" probabilistic principal component analysis (Tipping and Bishop 1999) "pFA" probabilistic factor analysis (Rubin and Thayer 1982) "pSimCCA" probabilistic similarity constrained canonical correlation analysis (Lahti et al. 2009) "TPriorpSimCCA" probabilistic similarity constarined canonical correlation analysis with possibility to tune T prior (Lahti et al. 2009) This parameter is only used if algorithm=pint.
scoreLimit float 0.1 Result cutoff limit. Only used if algorithm=pint.
transformType string "raw" Type of transformation which is applied when executing drsam algorithm. Must be one of "raw", "rank" or "standardize". Only used if algorithm=DRI and DRImethod=SAM.
windowSize int 10 Window size for pint algorithm sliding window. Only used if algorithm=pint.

Test cases

Test case Parameters IN
exprMatrix
IN
cnaMatrix
IN
exprAnnotation
IN
exprRefMatrix
IN
cnaRefMatrix
IN
labels
OUT
concomitantGenes
OUT
concomitantGenes2
OUT
plot
case1 properties exprMatrix cnaMatrix exprAnnotation (missing) (missing) (missing) concomitantGenes (missing) (missing)

algorithm=pint,
locusCol=loc

case3_edira properties exprMatrix cnaMatrix exprAnnotation exprRefMatrix cnaRefMatrix (missing) concomitantGenes (missing) (missing)

algorithm=edira,
locusCol=loc

case4 properties exprMatrix cnaMatrix exprAnnotation (missing) (missing) (missing) concomitantGenes (missing) (missing)

algorithm=pint,
windowSize=15,
fdrLimit=0.5,
pintArm=q,
locusCol=loc,

case5_SIM properties exprMatrix cnaMatrix exprAnnotation (missing) (missing) (missing) concomitantGenes (missing) (missing)

algorithm=SIM,
locusCol=loc

case6_SODEGIR properties exprMatrix cnaMatrix exprAnnotation (missing) (missing) (missing) (missing) (missing) (missing)

algorithm=SODEGIR,
perm = 10,
fdrLimit=1.0,
SGRthold=0.1,
locusCol=loc,
endCol=loc

case7_iCluster properties exprMatrix cnaMatrix exprAnnotation (missing) (missing) (missing) concomitantGenes (missing) plot

algorithm=iCluster,
locusCol=loc,
iClusterK=5

case8_int properties exprMatrix cnaMatrix exprAnnotation (missing) (missing) (missing) (missing) (missing) (missing)

algorithm=integrOmics,
locusCol=loc


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