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| chromstaR-package | Combinatorial and differential chromatin state analysis for ChIP-seq data |
| bin2dec | Conversion of decimal and binary states |
| binned.data | Binned read counts |
| binning | Convert aligned reads from various file formats into read counts in equidistant bins |
| binReads | Convert aligned reads from various file formats into read counts in equidistant bins |
| callPeaksMultivariate | Fit a Hidden Markov Model to multiple ChIP-seq samples |
| callPeaksReplicates | Fit a multivariate Hidden Markov Model to multiple ChIP-seq replicates |
| callPeaksUnivariate | Fit a Hidden Markov Model to a ChIP-seq sample. |
| callPeaksUnivariateAllChr | Fit a Hidden Markov Model to a ChIP-seq sample. |
| changeFDR | Adjust sensitivity of peak detection |
| changeMaxPostCutoff | Adjust sensitivity of peak detection |
| changePostCutoff | Change the posterior cutoff of a Hidden Markov Model |
| Chromstar | Wrapper function for the 'chromstaR' package |
| chromstaR | Combinatorial and differential chromatin state analysis for ChIP-seq data |
| chromstaR-objects | chromstaR objects |
| collapseBins | Collapse consecutive bins |
| combinatorialStates | Get the (decimal) combinatorial states of a list of univariate HMM models |
| combinedHMM | Combined multivariate HMM object |
| combinedMultiHMM | Combined multivariate HMM object |
| combineMultivariates | Combine combinatorial states from several Multivariates |
| conversion | Conversion of decimal and binary states |
| dec2bin | Conversion of decimal and binary states |
| differentialScoreMax | chromstaR scores |
| differentialScoreSum | chromstaR scores |
| dzinbinom | The Zero-inflated Negative Binomial Distribution |
| enrichmentAtAnnotation | Enrichment of (combinatorial) states for genomic annotations |
| enrichment_analysis | Enrichment analysis |
| experiment.table | Experiment data table |
| exportCombinations | Export genome browser uploadable files |
| exportCounts | Export genome browser uploadable files |
| exportFiles | Export genome browser uploadable files |
| exportGRangesAsBedFile | Export genome browser viewable files |
| exportPeaks | Export genome browser uploadable files |
| fixedWidthBins | Make fixed-width bins |
| genes_rn4 | Gene coordinates for rn4 |
| genomicFrequencies | Frequencies of combinatorial states |
| getCombinations | Get combinations |
| getDistinctColors | Get distinct colors |
| getStateColors | Get state colors |
| heatmapCombinations | Plot a heatmap of combinatorial states |
| heatmapCountCorrelation | Read count correlation heatmap |
| heatmapTransitionProbs | Heatmap of transition probabilities |
| loadHmmsFromFiles | Load 'chromstaR' objects from file |
| mergeChroms | Merge several 'multiHMM's into one object |
| model.combined | Combined multivariate HMM for demonstration purposes |
| model.multivariate | Multivariate HMM for demonstration purposes |
| model.univariate | Univariate HMM for demonstration purposes |
| multi.hmm | Multivariate HMM object |
| multiHMM | Multivariate HMM object |
| multivariateSegmentation | Multivariate segmentation |
| plotEnrichCountHeatmap | Enrichment analysis |
| plotEnrichment | Enrichment analysis |
| plotExpression | Overlap with expression data |
| plotFoldEnrichHeatmap | Enrichment analysis |
| plotGenomeBrowser | #' Plot a genome browser view #' #' Plot a simple genome browser view. This is useful for scripted genome browser snapshots. #' #' @param counts A 'GRanges-class' object with meta-data column 'counts'. #' @param peaklist A named list() of 'GRanges-class' objects containing peak coordinates. #' @param chr,start,end Chromosome, start and end coordinates for the plot. #' @param countcol A character giving the color for the counts. #' @param peakcols A character vector with colors for the peaks in 'peaklist'. #' @param style One of 'c('peaks', 'density')'. #' @param peakTrackHeight Relative height of the tracks given in 'peaklist' compared to the 'counts'. #' @return A 'ggplot' object. #' @examples #'## Get an example multiHMM ## #'file <- system.file("data","multivariate_mode-combinatorial_condition-SHR.RData", #' package="chromstaR") #'model <- get(load(file)) #'## Plot genome browser snapshot #'bins <- model$bins #'bins$counts <- model$bins$counts.rpkm[,1] #'plotGenomeBrowser(counts=bins, peaklist=model$peaks, #' chr='chr12', start=1, end=1e6) #' plotGenomeBrowser2 <- function(counts, peaklist=NULL, chr, start, end, countcol='black', peakcols=NULL, style='peaks', peakTrackHeight=5) ## Select ranges to plot ranges2plot <- reduce(counts[counts@seqnames == chr & start(counts) >= start & start(counts) <= end]) ## Counts counts <- subsetByOverlaps(counts, ranges2plot) if (style == 'peaks') df <- data.frame(x=(start(counts)+end(counts))/2, counts=counts$counts) # plot triangles centered at middle of the bin ggplt <- ggplot(df) + geom_area(aes_string(x='x', y='counts')) + theme(panel.grid = element_blank(), panel.background = element_blank(), axis.text.x = element_blank(), axis.title = element_blank(), axis.ticks.x = element_blank(), axis.line = element_blank()) maxcounts <- max(counts$counts) ggplt <- ggplt + scale_y_continuous(breaks=c(0, maxcounts)) else if (style == 'density') df <- data.frame(xmin=start(counts), xmax=end(counts), counts=counts$counts) ggplt <- ggplot(df) + geom_rect(aes_string(xmin='xmin', xmax='xmax', ymin=0, ymax=4, alpha='counts')) + theme(panel.grid = element_blank(), panel.background = element_blank(), axis.text = element_blank(), axis.title = element_blank(), axis.ticks = element_blank(), axis.line = element_blank()) else stop("Unknown value '", style, "' for parameter 'style'. Must be one of c('peaks', 'density').") ## Peaks if (!is.null(peaklist)) if (is.null(peakcols)) peakcols <- getDistinctColors(length(peaklist)) for (i1 in 1:length(peaklist)) p <- peakTrackHeight peaks <- subsetByOverlaps(peaklist[[i1]], ranges2plot) if (length(peaks) > 0) df <- data.frame(start=start(peaks), end=end(peaks), ymin=-p*i1, ymax=-p*i1+0.9*p) ggplt <- ggplt + geom_rect(data=df, mapping=aes_string(xmin='start', xmax='end', ymin='ymin', ymax='ymax'), col=peakcols[i1], fill=peakcols[i1]) trackname <- names(peaklist)[i1] df <- data.frame(x=start(counts)[1], y=-p*i1+0.5*p, label=trackname) ggplt <- ggplt + geom_text(data=df, mapping=aes_string(x='x', y='y', label='label'), vjust=0.5, hjust=0.5, col=peakcols[i1]) return(ggplt) Plot a genome browser view |
| plotHistogram | Histogram of binned read counts with fitted mixture distribution |
| plotHistograms | Histograms of binned read counts with fitted mixture distribution |
| plotting | chromstaR plotting functions |
| print.combinedMultiHMM | Print combinedMultiHMM object |
| print.multiHMM | Print multiHMM object |
| print.uniHMM | Print uniHMM object |
| pzinbinom | The Zero-inflated Negative Binomial Distribution |
| qzinbinom | The Zero-inflated Negative Binomial Distribution |
| readBamFileAsGRanges | Import BAM file into GRanges |
| readBedFileAsGRanges | Import BED file into GRanges |
| readConfig | Read chromstaR configuration file |
| readCustomBedFile | Read bed-file into GRanges |
| removeCondition | Remove condition from model |
| rzinbinom | The Zero-inflated Negative Binomial Distribution |
| scanBinsizes | Find the best bin size for a given dataset |
| scores | chromstaR scores |
| simulateMultivariate | Simulate multivariate data |
| simulateReadsFromCounts | Simulate read coordinates |
| simulateUnivariate | Simulate univariate data |
| state.brewer | Obtain combinatorial states from specification |
| stateBrewer | Obtain combinatorial states from experiment table |
| subsample | Normalize read counts |
| transitionFrequencies | Transition frequencies of combinatorial states |
| uni.hmm | Univariate HMM object |
| uniHMM | Univariate HMM object |
| unis2pseudomulti | Combine univariate HMMs to a multivariate HMM |
| variableWidthBins | Make variable-width bins |
| writeConfig | Write chromstaR configuration file |
| zinbinom | The Zero-inflated Negative Binomial Distribution |