Usage
PREDA_main(inputDataForPREDA, outputGenomicAnnotationsForPREDA
=NULL, nperms = 10000, verbose = TRUE, parallelComputations =
FALSE, multTestCorrection = "fdr", permutePerChromosome = FALSE,
blocksize = 10, permuteStatisticSign = FALSE, smoothMethod =
"lokern_scaledBandwidth_repeated", force = FALSE,
lokern_scaledBandwidthFactor = 2, limit.analysis = NULL)
Arguments
inputDataForPREDA
A Data for PREDA object
outputGenomicAnnotationsForPREDA
A GenomicAnnotationsForPREDA object.If NULL, GenomicsAnnotations for output data are obtained from
inputDataForPREDA
nperms
Number of permutations performed in PREDA analysis.
verbose
Logical, if TRUE some messages are printed concenrning the
advancement of the analysis.
parallelComputations
Logical, if TRUE Rmpi is used to spawn slave processes, thus
using parallel computing to speedup the analysis.
multTestCorrection
Multiple testing correction that will be adopted to correct the
statistic p-values. Possible values are "fdr", for benjamini and
Hochberg multiple testing correction and "qvalue" for p-values
correction performed with qvalue package.
permutePerChromosome
Logical, if TRUE data parmutations are perfored separatedly for
each chromsoome.
In most cases the default value (FALSE) is preferable to avoid
biases related to specific chromosomes extreme alterations.
blocksize
A parameter used to tune parallel computations if
parallelComputations is TRUE. This is actually the number of
permutations performed on each slave process before every
communication with master process.This is useftul to reduce the numebr of network communications
when slow communicatinos are established among slave processes.
permuteStatisticSign
Logical, if TRUE statistics signs are permuted instead of
permuting data along chromsomal position.
smoothMethod
The deafault smoothing metod used in the PREDA_main function is
lokern smoothing with scaled bandwidth, using a scaling factor
equal to 2.Possible values are "lokern", for standard
lokern smoothing, "quantsmooth", "spline" and
"runningmean.x", where x is a user defined value for the number
of adjacent data points using for running mean smoothing.
force
Logical, if TRUE force skipping quantsmooth control on
number of data points. Singe quantsmooth is very slow with a
high number of inpuit data, a check stopping computation with
more than 2000 data points in one or more chromosome was
introduced. This aprameter allow skippin this security check.
lokern_scaledBandwidthFactor
Factor of scaling for lokern estimated bandwidths
limit.analysis
Vector (numeric or character representing analyses names) to
limit the output of preda analysis to a subset of input analyses.