Man pages for raim/segmenTools
Tools for Functional Genome Exploration
| add_alphas | replace alpha values of an RGB string color vector |
| alignData | align genome data at specified coordinates (e.g. TSS) |
| annotateTarget | annotate target segments by overlapping query segments |
| annotationOverlap | analyze internal overlaps in a TRUE/FALSE feature annotation... |
| arno | Color Ramp Palette 'arno' |
| ash | asinh data transformation |
| bed2coor | parse a .bed format file |
| calculatePhase | calculate peak phase |
| ci95 | calculate 95 data vector using a t-distribution |
| circ.dens | circular density |
| clusterAnnotation | Cluster annotation enrichment scan |
| clusterAverages | calculates cluster averages |
| clusterCluster | calculates overlaps between two clusterings |
| clusterColors | get color vector for clustered features |
| clusterFlow | Alluvial plot for cluster matrices. |
| clusterProfile | Calculate biases of numerical data between clusterings. |
| clusterTimeseries2 | Cluster a processed time-series with k-means or flowClust |
| col2alpha | R colors with alpha value. |
| collapsePositions | collapse adjacent genome positions into segments |
| collectOvlStats | Collect statistics from from 'segmentAnnotate' |
| complex2degree | convert complex numbers to degrees |
| coor2bed | export internal coordinate format to bed file format |
| coor2index | convert chromosome coordinates to continuous index |
| degree2complex | convert phase (degree) to polar coordinates |
| dense2d | 2D density heatmap plot |
| expandCircularFeatures | Splits genome features spanning annotated ends of circular... |
| figlabel | Add sub-figure label to corners of plots |
| fillGenome | Get inter-segments |
| findAACodon | find genomic coordinates of amino acid position in a protein... |
| getChrSum | Generate chromosome index 'chrS' from lengths |
| get_fft | Discrete Fourier Transformation |
| getOverlapStats | Statistics of overlaps between two segment sets. |
| getSegmentClasses | splits segmenTier segment class strings into classes |
| getSegmentClassTable | splits segmenTier classes into a table |
| gff2tab | parse a GFF3 file into a table |
| idx2chr | get the chromosome from continuous index |
| idx2coor | Simple version of 'index2coor' for single values |
| idx2str | get the strand from continuous index |
| image_matrix | wrapper for 'image' plotting a data matrix in the orientation... |
| index2coor | convert continuous index to chromosome coordinates (reverse... |
| insertRows | insert rows as specified positions |
| jrplot | Jaccard vs. Ratio Segment Overlap Plots |
| lg2r | log2 ratio normalization |
| list2df | converts a names list of vectors of different length to a... |
| log_1 | log trafo handling zeros by adding 1 |
| logaxis | Logarithmic axis ticks |
| ma | moving average using 'filter' |
| meanzero | mean-0 normalization |
| mergeCluster | using 'flowMerge' to merge clusterings |
| mutatePositions | mutate positions in a string |
| normalize.los | LVS/LOS normalization |
| num2col | convert numeric values to color range: |
| parseAnnotation | Parse an annotation file (a bidirectional map) |
| parseAnnotationList | Parse a matrix of ID/annotation mappings |
| parseGEOSoft | parse GO Soft archives |
| parseJaccard | parses overlap statitics produced with bedtools |
| phaseDist | Calculates phase distributions |
| plotBIC | plot BIC from flowclusterTimeseries |
| plot_cdfLst | plot multiple cumulative distribution functions |
| plot.clusteraverages | plots cluster averages |
| plotClusterLegend | plot sorted clustering as color table |
| plotClusters | plots cluster averages |
| plotCor | scatter plot with correlation statistics |
| plotdev | Switch between plot devices |
| plotDFT | plot polar coordinates |
| plotOverlaps | plot cluster-cluster or segment-segment overlaps |
| plotOverlapsLegend | plot a legend for 'plotOverlaps' plots |
| plotSingles | plot indivividual time series in cluster context |
| presegment | Pre-segmentation of the time-series |
| pvalDist | cluster p-value summary |
| randomSegments | randomize locations of input segments |
| range2nt | calculates letter frequences in ranges of strings |
| readDist | distribution of read-counts, i.e., the mean, var, min&max and... |
| readFASTA | fasta sequence file parser adapted from (an older version of)... |
| reCluster | re-cluster clustering by 'kmeans' |
| relabelClusters | relabels cluster labels by their sorting |
| removeCircularFeatures | NOT WORKING - Undo 'expandCircularFeatures' searches for... |
| revcomp | calculate reverse complement of RNA or DNA |
| runGost | a wrapper for 'gprofiler2"s 'gost' function |
| segmentAnnotate | Overlaps between two sets of chromosome segments |
| segmentAverage | Average read-counts of segments |
| segmentMerge | merge genomic coordinates by type. |
| segmenTools | segmenTools : analysis of genome segmentations by segmenTier |
| segmentOverlaps | Jaccard-Index overlap test for classes of segments (genomic... |
| segmentOverlaps_bed | calculate segment overlap statistics using UCSC bedtools |
| segmentPrune | prune genomic coordinates at chromosome ends |
| segmentSort | sort genomic coordinates |
| segmentUpstream | get upstream or downstream range |
| selectColors | Map a distribution to a color scheme |
| selected | get clustering ID |
| seq2nt | calculate local nucleotide content |
| shadowtext | plot borders around text based on text colors |
| sortOverlaps | sorts cluster overlap structure by p-values |
| splitsegs | splits segments that span chromosome ends |
| summarizeGEOSoft | summarize GEOSoft probes |
| switchStrand | switches the strand information (reverse<->forward) of... |
| tab2gff | creates a gff3-like table |
| tagDuplicates | Tag duplicate names by increasing numbers. |
| t.clusterOverlaps | transpose cluster overlap object |
| testPhase | tests phase recovery by 'calculatePhase' |
| val2col | obselete, use 'num2col' |
| whichSegment | which segment covers a position |
| writeSegments | write out segment data to individual files |
| w.test | Wilcoxon test wrapper that returns a normalized U-statistic |
