create_RCNA_object() R function from [RCNA]

RCNA_object constructor

An S4 class used to specify parameters for an analysis run


create_RCNA_object(
  sample.names,
  ano.file,
  ncpu = 1,
  out.dir = tempdir(),
  file.coverage = NULL,
  gcParams = NULL,
  win.size = 75,
  gc.step = 0.01,
  file.raw.coverage = NULL,
  file.corrected.coverage = NULL,
  file.gc.factor = NULL,
  estimate_gc = TRUE,
  nkrParams = NULL,
  file.nkr.coverage = NULL,
  nkr = 0.9,
  x.norm = NULL,
  norm.cov.matrix = NULL,
  scoreParams = NULL,
  file.score.coverage = NULL,
  score.cutoff = 0.5,
  low.score.cutoff = NULL,
  high.score.cutoff = NULL,
  commands = list(),
  verbose = FALSE
)

Arguments

sample.names: Character vector containing names of subjects
ano.file: Character single file path detailing a feature-wise annotation file
ncpu: Numeric value specifying number of cores to use for analysis. Multiple cores will lead to parallel execution.
out.dir: Character vector containing the name of each subject's output directory
file.coverage: Character vector containing the path to the input coverage files for NKR and CNA score estimation.
gcParams: Data Frame storing all run parameters for the correct_gc_bias function. Can be specified by a file path to a CSV file, data.frame, or (if not specified) will be generated by other arguments.
win.size: Numeric value detailing the size of the sliding window used to calculate and detect correct GC-content correction.
gc.step: Numeric value detailing the size of each GC-content bin. If providing pre-calculated GC factor file this must match the bins in that file.
file.raw.coverage: Character vector containing the filename of the raw coverage files for GC-content correction. Must be used in combination with estimate_gc set to TRUE.
file.corrected.coverage: Character vector containing the filename of the corrected coverage files.
file.gc.factor: Character vector containing the filename of GC factor files. Used if and only if estimate_gc is set to FALSE.
estimate_gc: Logical that determines if GC bias factor is calculated. If set to TRUE then GC factor files will be generated for each sample. If set to FALSE then GC factor files must be supplied via file.gc.factor.
nkrParams: Data Frame storing all run parameters for the estimate_nkr function. Can be specified by a file path to a CSV file, data.frame, or (if not specified) will be generated by other arguments.
file.nkr.coverage: Character vector containing the filename of the input coverage file for NKR estimation. Defaults to file coverage if not specified.
nkr: Numeric between 0 and 1 which specifies the coverage quantile that should be considered a "normal" karyotype range for each position. Lowering this value may increase sensitivity but also Type I error.
x.norm: Logical vector with length equal to the length of sample.names, denoting whether each subject has to be X-normalized. Subjects with an XX karyotype should be set to TRUE to avoid double-counting the coverage on the X chromosome. Set to FALSE if chrX coverage is already normalized.
norm.cov.matrix: Character containing the directory or file name of the normalized coverage matrix. Generated by estimate_nkr if file doesn't exist.
scoreParams: Data Frame storing all run parameters for the estimate_feature_score function. Can be specified by a file path to a CSV file, data.frame, or (if not specified) will be generated by other arguments.
file.score.coverage: Character vector containing the input coverage file for the scoring function. Defaults to file.coverage if not specified.
score.cutoff: Numeric between 0 and 1 which specifies the score filter on the results file. This parameter creates a symmetrical cutoff around 0, filtering all results whose absolute value is less than the specified value. Non-symmetrical cutoffs can be specified using low.score.cutoff and high.score.cutoff.
low.score.cutoff: Numeric between 0 and 1 which specifies the lower score cutoff. Defaults to score.cutoff if not specified.
high.score.cutoff: Numeric between 0 and 1 which specifies the upper score cutoff. Defaults to score.cutoff if not specified.
commands: RCNA_analysis object storing commands and parameters from previous function runs on this object. For more information, see RCNA_analysis.
verbose: Show more messages and warnings. Useful for debugging.

Returns

A RCNA_object class object with the specified parameters.

Examples


# Create an example object - see \link{example_obj} for more information.
samples <- c("ex-sample-1", "ex-sample-2", "ex-sample-3")
ex.obj <- create_RCNA_object(sample.names = samples,
                    ano.file = system.file("examples" ,"annotations-example.csv", package = "RCNA"),
                    out.dir = "output",
                    file.raw.coverage = system.file("examples", "coverage",
                       paste0(samples, ".txt.gz"), package = "RCNA"),
                    norm.cov.matrix = file.path("output", "norm-cov-matrix.csv.gz"),
                    nkr = 0.9,
                    x.norm = "FALSE",
                    low.score.cutoff = -0.35,
                    high.score.cutoff = 0.35,
                    ncpu = 1)
class(ex.obj)

create_RCNA_object function

RCNA_object constructor

Arguments

Returns

Examples

See Also