Description Usage Arguments Details Value
This produces pathview plots of differentially expressed genes and their fold changes for given pathways.
1 2 | pathview_func(DEgenes, logFCcolumn = "logFC", pathway.id, out.suffix,
organism = "human")
|
DEgenes |
List of differentially expressed genes as output given by diff_limma_pairwise(). Rownames should be gene names (SMYBOLS). |
logFCcolumn |
Name of column that contains log fold change information. |
pathway.id |
KEGG pathway identification number. |
out.suffix |
Output suffix to be added to file name. |
organism |
Set organism. Defaults to human, can also be mouse. |
If you get the error message(s) data set 'korg' not found and/or data set 'bods' not found, it didn't properly extract these datasets from the pathview package. Run data(korg) and data(bods) manually!
Three output files are produced for each pathway: An .xml, a .png of the pathway and a .png of the pathway with DE genes and their fold change.
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