PCOPA
(Package: coGPS) :
P-value based outlier gene detection
Calculate P-value based statistics for outlier gene detection in dataset merged from multiple studies and give out outlier gene list for each patient.
● Data Source:
BioConductor
● Keywords:
● Alias: PCOPA
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Generate an outlier gene list for each patient restricted to the top PCOPA scored genes
● Data Source:
BioConductor
● Keywords:
● Alias: PatientSpecificGeneList
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PlotTopPCOPA
(Package: coGPS) :
Plot expression patterns of top ranked genes.
It first sorts the expression value exprslist[[i]]$exprs[j,] among the baseline samples(e.g. normal ones) and comparison group (e.g. tumor ones)seperately for selected gene j, and then plot the sorted expression values. The first argument exprslist should be the same one as for PCOPA; the second argument PCOPAresult should be an output of PCOPA; the third argument topcut determines how far we would go down the top ranked list; and the last argument typelist is a vector specifying the titles for each graph corresponds to a specific study.
● Data Source:
BioConductor
● Keywords:
● Alias: PlotTopPCOPA
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SampleData
(Package: coGPS) :
Sample Data for coGPS
Here we present an example of coGPS analysis.
● Data Source:
BioConductor
● Keywords:
● Alias: CNV_classlab_matched, CNV_exprs_matched, Exon_classlab_matched, Exon_exprs_matched, Hs.gmtl.c1, Methy_classlab_matched, Methy_exprs_matched
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coGPS internal
(Package: coGPS) :
coGPS package internal function.
These functions are not part of the package application programming interface and are not recommended to be used by the users.
● Data Source:
BioConductor
● Keywords:
● Alias: plotCOPA
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coGPS-package
(Package: coGPS) :
Cancer Outlier Gene Profile Sets
Gene Set Enrichment Analysis of P-value based statistics for outlier gene detection in dataset merged from multiple studies
● Data Source:
BioConductor
● Keywords: Microarray, Bioinformatics, DifferentialExpression
● Alias: coGPS, coGPS-package
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permCOPA
(Package: coGPS) :
Calculate PCOPA value for permuations
Run permutations by randomly shuffling the sample class labels and calculate a vector of PCOPA values for each permutation.
● Data Source:
BioConductor
● Keywords:
● Alias: permCOPA
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