Function reference • cisDynet

Add-ers Functions that add necessary annotation.
`addAnnotation()`	A function to add the necessary annotation for CAT.
`addFootprint()`	A function to add necessary annotation for foorprinting analysis.
Check-ers Functions that check necessary annotation.
`checkFTAnno()`	Check for the presence of footprint annotation files.
`checkGeAnno()`	Check for the presence of genome annotation files.
Cal-ers Functions for calculating.
`getClusterNum()`	A function to help you determine the cluster number before you use plotClusterSpecificPeak.
`getClusterTargetGenes()`	A function to find the target genes based on specific peaks.
`getCoaccessible()`	Get the co-accessible peaks in genome wide.
`getCount()`	A function to get the count file for chromVAR.
`getCountSplit()`	A function to get the count file for GWASNorm.
`getDiffPeak()`	A function to identify the differential peaks between two groups.
`getDiffTargetGenes()`	A function to call the differential peak target genes.
`getFootprintScore()`	A function to get the footprint score.
`getGeneBed()`	Get the specific gene coordinates and flanks.
`getGER()`	The function to integrate the GWAS enrichment results.
`getJasparMotifs2018()`	Get the motifs from JASPAR database (2018).
`getMotif2Gene()`	Convert motif ID to gene ID.
`getNetwork()`	Get the regulatory network.
`getPeak2Gene()`	Calculate the ATAC-to-RNA / Peak-to-Gene links.
`getRankMotif()`	Rank the motif deviation score.
`getSNP2Gene()`	A function help us look for which genes these SNPs might affect the expression of.
`getSpecificPeak()`	A function to identify sample specific peaks.
`getSuperEnhancer()`	A function to identify the super enahncers.
`getTimeATAC()`	Fitting the ATAC signal along the time.
`getTimeGene()`	Get the fitting time genes.
`getTimeRNA()`	Plot the RNA dynamic along the pseudo time.
`getTopSpecifcPeaks()`	Get the top N specific peaks in each sample.
`getTriads()`	A function to compare the chromatin accessibility across thress samples.
`getTriadsTargetGenes()`	A function to get the target genes of triads peak.
`get_beds()`	Read beds into list, can be arbitary dir_path.
`get_combine_result()`	Get intersection result which can be used as input of venn/upset plot.
`get_intersect()`	Update ident of bed_list based on intersection result
`get_overlap()`	Calculate the overlap interval.
`get_singlebed()`	Read beds into a single tibble.
`get_unique()`	Get distinctive records of A.
`get_upset_input()`	Get expression input which can be used in upset plot
`get_venn_key()`	Get keys which can be used in venn plot.
`annoMergedPeaks()`	Determining the merged peak category (Proximal/Distal/Intragenic). Determining the merged peak category (Proximal / Distal / Intragenic).
`annoPeaks()`	Annotating the peaks with ChIPSeeker.
`calc_dist_matrix()`	Calculate distance for matrix.
`calFisherPeaks()`	A function to calculate the two group peaks enrichment based on Fisher Test.
`calJSD()`	A function to calculate the JSD score.
`calPairwise()`	Calculate pairwised intersection of bed files.
`calSPM()`	A function to quantify tissue-specificity as the Specificity Measure (SPM).
`compareFootprints()`	A function to compare the Tn5 signal around the motif in the whole genome.
`GWASEnrichment()`	Do enrichment analysis with GWAS variants.
`GWASNorm()`	Preprocessing the data for GWAS enrichment.
Plotting Functions for plotting in cisDynet.
`plotClusterSpecificPeak()`	A function to help you plot the sample specific peaks with heatmap.
`plotCoGeneTracks()`	Plot specific gene ATAC signal and co-accessible with tracks.
`plotCoTracks()`	Plot genome tracks with co-accessible information.
`plotDendrogram()`	A function used to plot tree clustering result.
`plotDiffFootprint()`	Plot the differential footprint with Volcano, Bar or Lollipop.
`plotEnrich()`	A function to plot the enrichment rsult based on calFisherPeaks.
`plotFlower()`	Draw flower plot which represents the number of merged intervals.
`plotFootprintScore()`	A function to plot all samples footprint with scatter / heatmap.
`plotFootprintScoreExp()`	Plot the correlation of footprint score and TF expression.
`plotFragments()`	A function to plot the insertion fragment size.
`plotGeneTracks()`	Plot specific gene ATAC signal with tracks.
`plotGER()`	A function to plot the GWAS Enrichment Results.
`plotGO()`	A function to plot the every cluster target genes GO enrichment.
`plotGONetwork()`	A function to compare the GO enrichment result with Network.
`plotMA()`	A fucntion to plot MA plot
`plotNetwork()`	Plot the regulatory network.
`plotP2GHeatmap()`	Plot all the Peak2Gene links with heatmap.
`plotP2GTracks()`	Plot specific gene with tracks and peak2gene linkages.
`plotPCA()`	Plot the PCA plot based on quantification.
`plotPDI()`	Determining the peak category (Proximal/Distal/Intragenic).
`plotPeakGene()`	Plot one gene / one peak scatter plot.
`plotSpecificPeak()`	Plot the sample specific peaks.
`plotSummitDis()`	Plot the distance of peak summit to TSS.
`plotTimeAll()`	Plot the fitting time ATAC and RNA.
`plotTimeGene()`	Plot the specific gene expression along the time.
`plotTracks()`	Plot the genome signal with tracks.
`plotTriads()`	A function to plot the triads result.
`plotTSS()`	A function to plot the Tn5 signal around the TSSs.
`plotUpset()`	Draw upset plot of bed intersection.
`plotVenn()`	Draw venn plot of bed intersection.
`plotVolcano()`	A function to plot the differential result.
Others Other functions in cisDynet.
`logfile()`	Message with a timestamp.
`orderMatrix()`	Order the rows along with pseudo time.
`generate_windows()`	Generate window for a given bed file.
`makeSummarizedExperiment()`	Make SummarizedExperiment for chromVAR input.
`parse_bedpath()`	Parse bedpaths as file based path.
`quantile_normalization()`	Making quantile normalization for matrix.
`rowZscores()`	Scale matrix with Z-score.
`change_res_ident()`	Change identity of the beds$rec based on intersection result.
`flower_plot()`	Draw flower plot.
`init_result_df()`	Init dataframe which would be used in intersection results based on bed ident.
`loadBigWig()` `loadFullBigWig()`	loadBigWig

Reference

Add-ers

Check-ers

Cal-ers

Plotting

Others