PanNETsubtypesmRNA: PanNET subtyping based on mRNA expression data.
In syspremed/PanNETassigner: A cross-species analysis in pancreatic neuroendocrine tumors reveals molecular subtypes with distinctive clinical, metastatic, developmental, and metabolic characteristics.
Description
Usage
Arguments
Details
Value
Author(s)
References
Examples
Description
This function selects genes with standard deviation greater than 0.8, employs NMF to discover subtypes and SAM
to identify genes associated with the subtypes.
Usage
1
PanNETsubtypesmRNA(Indata)
Arguments
Indata
is PanNETsubtypesmRNA.Indata dataset which is mRNA expression data of tumors and islets. Genes are on the rows and the first column contain the gene names.
Details
The dataset used here, PanNETsubtypesmRNA.Indata, is core clinical mRNA/gene expression PanNET data of tumors and islets. Genes with standard deviation greater than 0.8, employs NMF to discover subtypes and SAM
to identify genes associated with the subtypes.
Value
The output of this function include NMF subtypes and SAM genes saved in your working directory under PanNetResults/mRNA folder.
Author(s)
Anguraj Sadanandam anguraj.sadanandam@icr.ac.uk
References
Anguraj Sadanandam, et all (2015). A cross-species analysis in pancreatic neuroendocrine tumors reveals molecular subtypes with distinctive clinical, metastatic, developmental, and metabolic characteristics. Cancer Discovery.
Examples
1
2
3
4
## Only one dataset required for this function
data(PanNETsubtypesmRNA.Indata)
## Run the function
PanNETsubtypesmRNA(PanNETsubtypesmRNA.Indata)
syspremed/PanNETassigner documentation built on May 31, 2019, 12:48 a.m.
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Description Usage Arguments Details Value Author(s) References Examples
Description
This function selects genes with standard deviation greater than 0.8, employs NMF to discover subtypes and SAM to identify genes associated with the subtypes.
Usage
1 | PanNETsubtypesmRNA(Indata)
|
Arguments
Indata |
is PanNETsubtypesmRNA.Indata dataset which is mRNA expression data of tumors and islets. Genes are on the rows and the first column contain the gene names. |
Details
The dataset used here, PanNETsubtypesmRNA.Indata, is core clinical mRNA/gene expression PanNET data of tumors and islets. Genes with standard deviation greater than 0.8, employs NMF to discover subtypes and SAM to identify genes associated with the subtypes.
Value
The output of this function include NMF subtypes and SAM genes saved in your working directory under PanNetResults/mRNA folder.
Author(s)
Anguraj Sadanandam anguraj.sadanandam@icr.ac.uk
References
Anguraj Sadanandam, et all (2015). A cross-species analysis in pancreatic neuroendocrine tumors reveals molecular subtypes with distinctive clinical, metastatic, developmental, and metabolic characteristics. Cancer Discovery.
Examples
1 2 3 4 | ## Only one dataset required for this function
data(PanNETsubtypesmRNA.Indata)
## Run the function
PanNETsubtypesmRNA(PanNETsubtypesmRNA.Indata)
|
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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