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Section 10: Combining output data with known cancer annotation
In case of cancer-related datasets, to facilitate the biological interpretability of the
enriched hubs, we provide a function
obtainCancerInfo
. This function maps the hubs
(corresponding to enriched modules) to the catalogue of genes already causally
associated with cancer(s), provided the catalogue file is provided as an input parameter
in Excel format. For example, to determine whether hubs (associated with enriched
modules) in the output file
Gene_Output_1.txt
(Section 2) correspond to known cancer
genes, at the R command prompt type
obtainCancerInfo(hubFile = "Gene_Output_1.txt"
, cancerAnnotationFile = "Cancer_Gene_Census.xls"
, outFile = "Hub_CIC_Info.txt")
The output file
Hub_CIC_Info.txt
contains hubs (with unadjusted p-value < 0.05) that
map to known cancer genes.
Unlike the microRNA interactomes which are updated regularly in the
VANData
package, the
Cancer_Gene_Census
file is for example purposes only and is not updated.
Therefore, we encourage the user to download the most up-to-date version of the
annotation file from the website
http://www.sanger.ac.uk/genetics/CGP/Census/
prior to
executing this R function.
Summary of Contents for GLSY22522
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