segmByCluster: Multicore Genome Segmentation Program

Description Usage Arguments Value

Description

This program segments DNA copy number data into regions of estimated equal copy number using circular binary segmentation (CBS) (DNAcopy package) and multicore (doParallel).

Usage

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segmByCluster(x, weights = NULL, alpha = 0.01, nperm = 10000,
  p.method = c("hybrid", "perm"), min.width = 2, kmax = 25, nmin = 200,
  eta = 0.05, sbdry = NULL, trim = 0.025, undo.splits = c("none",
  "prune", "sdundo"), undo.prune = 0.05, undo.SD = 2, verbose = 1,
  cluster = getDoParWorkers())

Arguments

x

an object of class CNA

weights

a vector of weights for the probes. The weights should be inversely proportional to their variances. Currently all weights should be positive i.e. remove probes with zero weight prior to segmentation.

alpha

significance levels for the test to accept change-points.

nperm

number of permutations used for p-value computation.

p.method

method used for p-value computation. For the "perm" method the p-value is based on full permutation. For the "hybrid" method the maximum over the entire region is split into maximum of max over small segments and max over the rest. Approximation is used for the larger segment max. Default is hybrid.

min.width

the minimum number of markers for a changed segment. The default is 2 but can be made larger. Maximum possible value is set at 5 since arbitrary widths can have the undesirable effect of incorrect change-points when a true signal of narrow widths exists.

kmax

the maximum width of smaller segment for permutation in the hybrid method.

nmin

the minimum length of data for which the approximation of maximum statistic is used under the hybrid method. should be larger than 4*kmax

eta

the probability to declare a change conditioned on the permuted statistic exceeding the observed statistic exactly j (= 1,...,nperm*alpha) times.

sbdry

the sequential boundary used to stop and declare a change. This boundary is a function of nperm, alpha and eta. It can be obtained using the function "getbdry" and used instead of having the "segment" function compute it every time it is called.

trim

proportion of data to be trimmed for variance calculation for smoothing outliers and undoing splits based on SD.

undo.splits

A character string specifying how change-points are to be undone, if at all. Default is "none". Other choices are "prune", which uses a sum of squares criterion, and "sdundo", which undoes splits that are not at least this many SDs apart.

undo.prune

the proportional increase in sum of squares allowed when eliminating splits if undo.splits="prune".

undo.SD

the number of SDs between means to keep a split if undo.splits="sdundo".

verbose

level of verbosity for monitoring the program's progress where 0 produces no printout, 1 prints the current sample, 2 the current chromosome and 3 the current segment. The default level is 1.

cluster

A specification appropriate to the type of cluster.

Value

See details segment and makeCluster


AlexeiSleptcov/aggi documentation built on May 5, 2019, 4:53 a.m.