expr_dist: Expression Distance.
In hyginn/BCB420.2019.ESA: Exploratory Systems Analysis Tools

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

expr_dist calculates the pairwise distance of gene expression profiles.

1	expr_dist(gene1, gene2, profiles)

`gene1`	Character, HGNC symbol of the first gene.
`gene2`	Character, HGNC sysmbol of the second gene
`profiles`	Matrix of expression profiles, generated by calling `fetchData("GEOprofiles")`

Similarity between 2 expression profiles is calculated by taking the absolute value of the Spearman correlation. Spearman correlation is used because we do not care whether the correlation is linear. Absolute value ensures that both strong positive and negative correlations result in high similarity. Distance is then taken as 1 - similarity. Distance is returned as 1 (maximum possible) if the expression profile for either gene is unavailable.

Numeric, distance score.

Rachel Silverstein (aut)

See fetchData for the format of expression profiles used by this function.

## Not run: 
# Find the distance between the expression profiles of BRCA1 and BRCA2
GEO <- fetchData("GEOprofiles")
expr_dist("BRCA1", "BRCA2", GEO)

## End(Not run)