rubic: Create a new RUBIC object

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

Description

With this function it is possibile to create and initialize a new RUBIC object.

Usage

rubic(fdr, seg.cna, markers, 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, ...)

Arguments

fdr	A number indicating the wanted event based false descovery rate. For example 0.25.
seg.cna	Either a character string naming a file or a data.table containing the segmented CNA data in appropriate format. In case a file name is provided the file will be open and read as a data.table.
markers	Either a character string naming a file or a data.table containing the markers informations in appropriate format. In case a file name is provided the file will be opened and read as a data.table.
samples	Either a character string naming a file or a character vector containing the sample IDs used for the analysis. In case a file name is provided the file will be open and read as a data.table. In case this parameter is not specified, all the samples presents in the seg.cna file will be used.
genes	Either a character string naming a file or a data.table containing the gene locations in appropriate format. In case a file name is provided the file will be open and read as a data.table. In case this parameter is not specified, RUBIC will attempt to download the most recent annotations using Biomart.
amp.level	A positive number specifying the threshold used for calling amplifications. The default value is set to 0.1.
del.level	A negative number specifying the threshold used for calling deletions. The default value is set to -0.1.
min.seg.markers	A positive integer specifying the number of probes allowed in each segment. The default value is set to 1, which means that no segments will be merged. If this parameter is set to a number larger than 1, all segments with less than min.seg.markers will be joined with adjacent segments until a segment with at least min.seg.markers will be formed.
min.mean	A number specifying the minimum mean copy number allowed. By default segments will not be filtered based on their minimum mean copy number.
max.mean	A number specifying the maximum mean copy number allowed. By default segments will not be filtered based on their maximum mean copy number.
min.probes	The minimum number of probes to be considered in the analysis.
focal.threshold	The maximum length of a recurrent region to be called focal. Only regions smaller than focal.threshold bases will be called focal. By default 10000000 bases.
seg.cna.header	A logical value indicating whether the seg.cna file contains the names of the variables as its first line. The default is set to TRUE.
markers.header	A logical value indicating whether the markers file contains the names of the variables as its first line. The default is set to TRUE.
samples.header	A logical value indicating whether the samples file contains the names of the variables as its first line. Please notice that while the default value of seg.cna.header and markers.header is set to TRUE, RUBIC do not expect an header by default for the samples file (and therefore this value is set by default to FALSE).
col.sample	The number of the column contaning the sample name in the seg.cna file. By default RUBIC expect the sample name to be in the 1st column.
col.chromosome	The number of the column contaning the chromosome name in the seg.cna file. By default RUBIC expect the chromosome name to be in the 2nd column.
col.start	The number of the column contaning the start position of each segment in the seg.cna file. By default RUBIC expect the start position to be in the 3rd column.
col.end	The number of the column contaning the end position of each segment in the seg.cna file. By default RUBIC expect the the end position to be in the 4th column.
col.log.ratio	The number of the column contaning the log.ratio name in the seg.cna file. By default RUBIC expect the log.ratio to be in the 6th column.
...	Additional arguments to be passed to the constructor. Reserved for future use.

Details

In order to use the RUBIC method it is necessary to create e initialize a new RUBIC object using data and parameters specific to your analysis. This function reads and preprocess all the data and returns an object of the RUBIC class. It is possibile to start the analysis using the method estimate.parameters or any other method of the RUBIC class.

Value

A new RUBIC object.

See Also

RUBIC-class

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