RUBIC-class: RUBIC Class

In NKI-CCB/RUBIC: Recurrent DNA copy number break detection to identify driver aberrations

Description

A ReferenceClass that contains all the data needed and generated by the RUBIC algorithm.

Details

It is possibile and recommended to instanciate a new RUBIC object by using the convenience function rubic.

Fields

fdr

Event based false descovery rate.

genes

A data.table containg the gene locations.

samples

A character vector containing sample IDs.

markers

A data.table containing the markers informations.

map.loc

A data table containing the markers mapped on the segments.

min.mean

The minimum mean copy number allowed.

max.mean

The maximum mean copy number allowed.

min.probes

The minimum number of probes to be considered in the analysis.

min.seg.markers

The number of probes allowed in each segment.

amp.level

The threshold used for calling amplifications.

del.level

The threshold used for calling deletions.

focal.threshold

The maximum length of a recurrent region to be called focal.

Methods

call.events()

Call recurrent events.

call.focal.events(genes = NULL)

Call focal events.

estimate.parameters(quiet = T, test.env = NULL)

Estimate the parameters necessary for segmentation and event calling.

initialize(fdr = NULL, seg.cna = NULL, markers = NULL, samples = NULL, genes = NULL, amp.level = 0.1, del.level = -0.1, min.seg.markers = 1, min.mean = NA_real_, max.mean = NA_real_, min.probes = 260000, focal.threshold = 1e+07, seg.cna.header = T, markers.header = T, samples.header = F, col.sample = 1, col.chromosome = 2, col.start = 3, col.end = 4, col.log.ratio = 6, ...)

Create a new RUBIC object. It is recommended to use the rubic function instead of calling this method directly. See rubic for parameter descriptions.

save(file)

Save the current state of the RUBIC object to file.

save.focal.gains(file)

Save focal gains to a file in TSV format.

save.focal.losses(file)

Save focal losses to a file in TSV format.

save.plots(dir, genes = NULL, steps = T, width = 11, height = 5)

Save gains and losses plots for each chromosome.

segment()

Generate positive and negative segments.

See Also

rubic

NKI-CCB/RUBIC documentation built on Dec. 17, 2021, 5:17 a.m.