enrichmentAtAnnotation {chromstaR} | R Documentation |
The function calculates the enrichment of a genomic feature with peaks or combinatorial states. Input is a multiHMM
object (containing the peak calls and combinatorial states) and a GRanges-class
object containing the annotation of interest (e.g. transcription start sites or genes).
enrichmentAtAnnotation(bins, info, annotation, bp.around.annotation = 10000, region = c("start", "inside", "end"), what = "combinations", num.intervals = 21, statistic = "fold")
bins |
The |
info |
The |
annotation |
A |
bp.around.annotation |
An integer specifying the number of basepairs up- and downstream of the annotation for which the enrichment will be calculated. |
region |
A combination of |
what |
One of |
num.intervals |
Number of intervals for enrichment 'inside' of annotation. |
statistic |
The statistic to calculate. Either 'fold' for fold enrichments or 'fraction' for fraction of bins falling into the annotation. |
A list()
containing data.frame()
s for enrichment of combinatorial states and binary states at the start, end and inside of the annotation.
Aaron Taudt