tf_dist: Transcription Factor Distance
In hyginn/BCB420.2019.ESA: Exploratory Systems Analysis Tools

Description Usage Arguments Details Value Author(s) See Also Examples

tf_dist Calculate upstream transcription factor binding site distance between 2 genes.

1	tf_dist(gene1, gene2, geneList)

`gene1`	String, HGNC symbol for the first gene.
`gene2`	String, HGNC symbol for the second gene.
`geneList`	A list of lists of transcription factors than have binding sites upstream of genes. Generated by calling `fetchData("GTRDgeneTFs")`.

Calculate the distance/dissimilarity of upstream transcription factors of 2 genes. Similarity is taken to be the Jaccard Index of the set overlap between the 2 transcription factors sets. Distance is then taken to be 1 - similarity.

The similarity score of gene1 and gene2: number of shared upstream transcription factors.

Rachel Silverstein (aut)

fetchData For format of geneList

# Calculate the transcription factor distance of 2 related genes "BRCA1" and "BRCA2"
## Not run: 
geneList <- fetchData("GTRDgeneTFs")
tf_dist("BRCA1", "BRCA2", geneList)

## End(Not run)