Man pages for raim/segmenTools
Analysis of Genome Segmentations by segmenTier

add_alphasreplace alpha values of an RGB string color vector
alignDataalign genome data at specified coordinates (e.g. TSS)
annotateTargetannotate target segments by overlapping query segments
ashasinh data transformation
calculatePhasecalculate peak phase
ci95calculate 95 data vector using a t-distribution
circ.denscircular density
clusterAnnotationclustering enrichment scan
clusterAveragescalculates cluster averages
clusterClustercalculates overlaps between two clusterings
clusterColorsget color vector for clustered features
clusterTimeseries2Cluster a processed time-series with k-means or flowClust
collectOvlStatsCollect statistics from from 'segmentOverlap'
complex2degreeconvert complex numbers to degrees
coor2indexconvert chromosome coordinates to continuous index
dense2d2D density heatmap plot
expandCircularFeaturesSplits genome features spanning annotated ends of circular...
fillGenomeGet inter-segments
findAACodonfind genomic coordinates of amino acid position in a protein...
getChrSumGenerate chromosome index 'chrS' from lengths
get_fftDiscrete Fourier Transformation
getOverlapStatsStatistics of overlaps between two segment sets.
getSegmentClassessplits segmenTier segment class strings into classes
getSegmentClassTablesplits segmenTier classes into a table
gff2tabparse a GFF3 file into a table
idx2chrget the chromosome from continuous index
idx2coorSimple version of 'index2coor' for single values
idx2strget the strand from continuous index
image_matrixwrapper for 'image' plotting a data matrix in the orientation...
index2coorconvert continuous index to chromosome coordinates (reverse...
insertRowsinsert rows as specified positions
lg2rlog2 ratio normalization
log_1log trafo handling zeros by adding 1
mamoving average using 'filter'
meanzeromean-0 normalization
mergeClusterusing 'flowMerge' to merge clusterings
parseAnnotationparse an annotation file (a bidirectional map)
parseGEOSoftparse GO Soft archives
phaseDistCalculates phase distributions
plotBICplot BIC from flowclusterTimeseries
plot_cdfLstplot multiple cumulative distribution functions
plot.clusteraveragesplots cluster averages
plotClusterLegendplot sorted clustering as color table
plotClustersplots cluster averages
plotdevSwitch between plot devices
plotDFTplot polar coordinates
plotOverlapsplot cluster-cluster or segment-segment overlaps
plotSinglesplot indivividual time series in cluster context
presegmentPre-segmentation of the time-series
pvalDistcluster p-value summary
randomSegmentsrandomize locations of input segments
range2ntcalculates letter frequences in ranges of strings
readDistdistribution of read-counts, i.e., the mean, var, min&max and...
reClusterre-cluster clustering by 'kmeans'
relabelClustersrelabels cluster labels by their sorting
removeCircularFeaturesNOT WORKING - Undo 'expandCircularFeatures' searches for...
revcompcalculate reverse complement of RNA or DNA
segmentAverageAverage read-counts of segments
segmentJaccardJaccard-Index overlap test for classes of segments (genomic...
segmenToolssegmenTools : analysis of genome segmentations by segmenTier
segmentOverlapOverlaps between two sets of chromosome segments
selectedget clustering ID
seq2ntcalculate local nucleotide content
sortOverlapssorts cluster overlap structure by p-values
splitsegssplits segments that span chromosome ends
summarizeGEOSoftsummarize GEOSoft probes
switchStrandswitches the strand information (reverse<->forward) of...
tab2gffcreates a gff3-like table
tagDuplicatesTag duplicate names by increasing numbers.
testPhasetests phase recovery by 'calculatePhase'
whichSegmentwhich segment covers a position
writeSegmentswrite out segment data to individual files
raim/segmenTools documentation built on Feb. 12, 2019, 3:46 a.m.