RCP | R Documentation |
Produce a dataframe with the probabilities of contacts in a set of distance-bins. Bins are created on a log scale, which leads to equal amounts of datapoints per bin.
RCP(
explist,
bedlist = NULL,
chromsToUse = NULL,
maxDistance = NULL,
genomeWide = NULL
)
explist |
List of GENOVA contacts-objects from 'load_contacts()'. |
bedlist |
A named list of BED-like dataframes of the regions of interest. |
chromsToUse |
A vector containing the chromosome-names of interest. |
maxDistance |
The maximal distance to calculate RCPs for. |
genomeWide |
Normalise with genome-wide counts or per-chromosome (default). |
An RCP_discovery object containing:
raw |
a per-distance probability |
smooth |
a log10-mean smoothed probability |
40kb-500kb
Robin H. van der Weide, r.vd.weide@nki.nl
# Calculate the RCP of chromosome 1
## Not run:
RCP_out = RCP(experimentList = list('WT' = WT_1MB), chromsToUse = 'chr1')
# Plot the RCP
visualise(RCP_out)
## End(Not run)
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