Description Usage Arguments Details Value Author(s) References Examples
This function selects PanNETassinger-mRNA signature from the gene expression validation dataset. NMF is employed to indentify PanNET subtypes using this dataset.
1 | PanNETsubtypesmRNAVal(Indata, IndSAMdata)
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Indata |
PanNETsubtypesmRNAVal.Indata is the gene expression validation dataset. Genes are on the rows and the first column contain the gene names. |
IndSAMdata |
PanNETsubtypesmRNAVal.IndSAMdata contain 221 PanNETassigner-mRNA signature for finding the PanNET subtypes. |
The 221 PanNETassigner-mRNA signature in PanNETsubtypesmRNAVal.IndSAMdata is selected from PanNETsubtypesmRNAVal.Indata, gene expression validation dataset, and NMF is used to discover PanNET mRNA expression subtypes in this dataset.
The output of this function include NMF mRNA expression subtypes saved in your working directory under PanNetResults/mRNAVal folder.
Anguraj Sadanandam anguraj.sadanandam@icr.ac.uk
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.
1 2 3 4 5 | ### Two datasets are required for this function
data(PanNETsubtypesmRNAVal.Indata)
data(PanNETsubtypesmRNAVal.IndSAMdata)
### Run the function
PanNETsubtypesmRNAVal(PanNETsubtypesmRNAVal.Indata,PanNETsubtypesmRNAVal.IndSAMdata)
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