getScores: Get CHiCAGO scores.
In Chicago: CHiCAGO: Capture Hi-C Analysis of Genomic Organization

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

Converts p-values into a CHiCAGO score, using p-value weighting.

1 2	getScores(cd, method = "weightedRelative", includeTrans = TRUE, plot = TRUE, outfile = NULL)

`cd`	A `chicagoData` object.
`method`	Either "weightedRelative" (recommended), or "unweighted".
`includeTrans`	If `FALSE`, trans interactions are discounted.
`plot`	Plot a diagnostic plot.
`outfile`	A string containing a .pdf file location to write to.

Weighting is performed using the parameters weightAlpha, weightBeta, weightGamma, weightDelta. Briefly, this function calculates weights w that decrease with increasing distance. Then, we construct weighted p-values p/w. As a result, the significance of long-range interactions is upweighted, and the significance of short-range interactions is downweighted.

Finally, the output score is calculated as -log(p/w) - log(w_max), where w_max is the highest attainable weight, and provided the score is positive (otherwise it is set to 0).

Please see the CHiCAGO paper and its supplementary for full details.

An object of class chicagoData.

The object intData(cd) is updated by reference. Thus, intData(cd) will be altered. See vignette for further information.

Jonathan Cairns

Genovese, C. R., Roeder, K., and Wasserman, L. (2006). False discovery control with p-value weighting. Biometrika, 93, 509-524. doi:10.1093/biomet/93.3.509

chicagoPipeline

data(cdUnitTest)

##modifications to cdUnitTest, ensuring it uses correct design directory
designDir <- file.path(system.file("extdata", package="Chicago"), "unitTestDesign")
cdUnitTest <- modifySettings(cd=cdUnitTest, designDir=designDir)

cdUnitTest <- getScores(cdUnitTest)