segmenTier (version 0.1.2)

segmentCluster.batch: Batch wrapper for segmentClusters.

Description

A high-level wrapper for multiple runs of segmentation by segmentClusters for multiple clusterings and/or multiple segmentation parameters. It additionally allows to tag adjacent segments to be potentially fused due to similarity of their clusters.

Usage

segmentCluster.batch(cset, varySettings = setVarySettings(),
  fuse.threshold = 0.2, rm.nui = TRUE, type.name, short.name = TRUE,
  id, save.matrix = FALSE, verb = 1)

Arguments

cset

a clustering set as returned by clusterTimeseries

varySettings

list of settings where each entry can be a vector; the function will construct a matrix of all possible combinations of parameter values in this list, call segmentClusters for each, and report a matrix of segments where the segment `type' is constructed from the varied parameters; see option short.name. A varySettings list with all required (default) parameters can be obtained via function setVarySettings.

fuse.threshold

if adjacent segments are associated with clusters the centers of which have a Pearson correlation >fuse.threshold the field "fuse" will be set to 1 for the second segments (top-to-bottom as reported)

rm.nui

remove nuisance cluster segments from final results

type.name

vector of strings selecting the parameters which will be used as segment types. Note, that all parameters that are actually varied will be automatically added (if missing). The list can include parameters from time-series processing found in the "clustering" object cset as cset$tids.

short.name

default type name construction; if TRUE (default) parameters that are not varied will not be part of the segment type and ID. This argument has no effect if argument type.name is set.

id

if set, the default segment IDs, constructed from numbered segment types, are replaced by this

save.matrix

store the total score matrix S(i,c) and the backtracing matrix K(i,c); useful in testing stage or for debugging or illustration of the algorithm; TODO: save.matrix is currently not implemented, since batch function returns a matrix only

verb

level of verbosity, 0: no output, 1: progress messages

Value

Returns an object of class "segments", just as its base function segmentClusters, but the main segment table, list item "segments", is a data.frame with additional columns "ID" and "type", automatically generated strings indicating the used parameters (each "type" reflects one parameter set), and "colors", indicating the automatically generated color of the assigned cluster label.

Details

This is a high-level wrapper for segmentClusters which allows segmentation over multiple clusterings as provided by the function clusterTimeseries and over multiple segmentation parameters. Each parameter in the list varySettings can be a vector and ALL combinations of the passed parameter values will be used for one run of segmentClusters. The resulting segment table, list item "segments" of the returned object, is a data.frame with additional columns "ID" and "type", automatically generated strings indicating the used parameters (each "type" reflects one parameter set), and "colors", indicating the automatically generated color of the assigned cluster label.

Examples

# NOT RUN {
# load example data, an RNA-seq time-series data from a short genomic
# region of budding yeast
data(primseg436)

# 1) Fourier-transform time series:
tset <- processTimeseries(ts=tsd, na2zero=TRUE, use.fft=TRUE,
                          dft.range=1:7, dc.trafo="ash", use.snr=TRUE)

# 2) cluster time-series several times into K=12 clusters:
cset <- clusterTimeseries(tset, K=c(12,12,12))

# 3) choose parameter ranges, here only E is varied 
vary <- setVarySettings(M=100, E=c(1,3), nui=3, S="icor", Mn=20)

# 4) ... segment ALL using the batch function:
# }
# NOT RUN {
 ## NOTE: takes too long for CRAN example timing restrictions
segments <- segmentCluster.batch(cset=cset, varySettings=vary)

# 5) inspect results:
print(segments)
plotSegmentation(tset, cset, segments)

# 6) and get segment border table. Note that the table has
#    additional columns "ID" and "type", indicating the used parameters,
#    and "color" providing the color of the cluster the segment was
#    assigned to. This allows to track segments in the inspection plots.
sgtable <- segments$segments
# }
# NOT RUN {
# }