CiberAMP.classifier: Perform joint expression and copy-number variation analyses...
In vqf/ciberAMP: mRNA and copy number data integrative algorithm.
CiberAMP.classifier R Documentation
Perform joint expression and copy-number variation analyses on a set of genes using a set of tumor samples.
Description
Perform joint expression and copy-number variation analyses on a set of genes using a set of tumor samples.
Usage
CiberAMP.classifier(res1 = NULL, res3 = NULL, width.window = 1e+06)
Arguments
res1
The first resulting data frame from CiberAMP outcomes
res3
The third resulting data frame from CiberAMP outcomes
width.window
Number of base pairs to be analyzed in order to define genomic clusters
Value
List containing four data frames:
1 - Top candidates: SCN-associated DEGs with no co-amplification/deletion with a known oncogene and OUTSIDE a genomic cluster
2 - Second best candidates: SCN-associated DEGs with no co-amplification/deletion with a known oncogene and INSIDE a genomic cluster
3 - Third best candidates: SCN-associated DEGs co-amplified/deleted with a known oncogene and OUTSIDE a genomic cluster. This may contain COSMIC CGC oncogenes.
4 - Fourth best candidates: SCN-associated DEGs co-amplified/deleted with a known oncogene and INSIDE a genomic cluster. This contains COSMIC CGC oncogenes.
vqf/ciberAMP documentation built on April 12, 2022, 12:45 p.m.
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| CiberAMP.classifier | R Documentation |
Perform joint expression and copy-number variation analyses on a set of genes using a set of tumor samples.
Description
Perform joint expression and copy-number variation analyses on a set of genes using a set of tumor samples.
Usage
CiberAMP.classifier(res1 = NULL, res3 = NULL, width.window = 1e+06)
Arguments
res1 |
The first resulting data frame from CiberAMP outcomes |
res3 |
The third resulting data frame from CiberAMP outcomes |
width.window |
Number of base pairs to be analyzed in order to define genomic clusters |
Value
List containing four data frames: 1 - Top candidates: SCN-associated DEGs with no co-amplification/deletion with a known oncogene and OUTSIDE a genomic cluster 2 - Second best candidates: SCN-associated DEGs with no co-amplification/deletion with a known oncogene and INSIDE a genomic cluster 3 - Third best candidates: SCN-associated DEGs co-amplified/deleted with a known oncogene and OUTSIDE a genomic cluster. This may contain COSMIC CGC oncogenes. 4 - Fourth best candidates: SCN-associated DEGs co-amplified/deleted with a known oncogene and INSIDE a genomic cluster. This contains COSMIC CGC oncogenes.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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