Additional functions for working with ChIP-Seq data
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Documentation for package ‘extraChIPs’ version 1.8.1
Help Pages
| addDiffStatus | Add a status column |
| addDiffStatus-method | Add a status column |
| as_tibble | Convert to a tibble |
| as_tibble.DataFrame | Convert to a tibble |
| as_tibble.GenomicRanges | Convert to a tibble |
| as_tibble.GInteractions | Convert to a tibble |
| as_tibble.Seqinfo | Convert to a tibble |
| as_tibble.SummarizedExperiment | Convert to a tibble |
| as_tibble.TopTags | Convert to a tibble |
| bestOverlap | Find the best overlap between GRanges |
| bestOverlap-method | Find the best overlap between GRanges |
| chopMC | Keep unique ranges and collapse mcols |
| collapseGenes | Collapse a vector of gene names |
| colToRanges | Coerce a column to a GRanges object |
| colToRanges-method | Coerce a column to a GRanges object |
| cytobands | Cytogenetic bands |
| defineRegions | Define Genomic Regions Based on Gene Annotations |
| defineSeqinfo | Use package data to define a Seqinfo object |
| distinctMC | Keep distinct ranges and mcols |
| dualFilter | Apply two filters to sliding windows |
| ex_datasets | Datasets for an example region |
| ex_genes | Datasets for an example region |
| ex_hic | Datasets for an example region |
| ex_prom | Datasets for an example region |
| ex_trans | Datasets for an example region |
| fitAssayDiff | Detect Differential ChIP Signal |
| fitAssayDiff-method | Detect Differential ChIP Signal |
| fixed_width_datasets | Datasets for the Fixed-Width Vignette |
| getProfileData | Get Profile Data surrounding specified ranges |
| getProfileData-method | Get Profile Data surrounding specified ranges |
| grch37.cytobands | Cytogenetic bands |
| grch38.cytobands | Cytogenetic bands |
| grlToSE | Set columns from a GRangesList as Assays in a SummarizedExperiment |
| grlToSE-method | Set columns from a GRangesList as Assays in a SummarizedExperiment |
| importPeaks | Import peaks |
| intersectMC | Perform set operations retaining mcols |
| intersectMC-method | Perform set operations retaining mcols |
| makeConsensus | Make a set of consensus peaks |
| mapByFeature | Map Genomic Ranges to genes using defined features |
| mapGrlCols | Collapse a GRangesList adding multiple columns from each element |
| mergeByCol | Merge sliding windows using a specified column |
| mergeByCol-method | Merge sliding windows using a specified column |
| mergeByHMP | Merge Sliding Windows using the Harmonic Mean P |
| mergeByHMP-method | Merge Sliding Windows using the Harmonic Mean P |
| mergeBySig | Merge overlapping ranges based on p-values |
| mergeBySig-method | Merge overlapping ranges based on p-values |
| partitionRanges | Partition a set of Genomic Ranges |
| partitionRanges-method | Partition a set of Genomic Ranges |
| peaks | Datasets for the Fixed-Width Vignette |
| plotAssayDensities | Plot Densities for any assay within a SummarizedExperiment |
| plotAssayDensities-method | Plot Densities for any assay within a SummarizedExperiment |
| plotAssayHeatmap | Draw a heatmap from a single SummarizedExperiment assay |
| plotAssayHeatmap-method | Draw a heatmap from a single SummarizedExperiment assay |
| plotAssayPCA | Plot PCA For any assay within a SummarizedExperiment |
| plotAssayPCA-method | Plot PCA For any assay within a SummarizedExperiment |
| plotAssayRle | Plot RLE for a given assay within a SummarizedExperiment |
| plotAssayRle-method | Plot RLE for a given assay within a SummarizedExperiment |
| plotGrlCol | Draw a plot from a GRangesList column |
| plotHFGC | Plot a Genomic Region showing HiC, Features, Genes and Coverage |
| plotOverlaps | Plot Overlaps Between List Elements |
| plotOverlaps-method | Plot Overlaps Between List Elements |
| plotPairwise | Plot Pairwise Values from a GRangeList |
| plotPie | Draw Pie Graphs based on one or more columns |
| plotPie-method | Draw Pie Graphs based on one or more columns |
| plotProfileHeatmap | Draw a coverage Profile Heatmap |
| plotProfileHeatmap-method | Draw a coverage Profile Heatmap |
| plotSplitDonut | Draw Two-Level Donut Charts |
| plotSplitDonut-method | Draw Two-Level Donut Charts |
| propOverlap | Find the proportions of an overlapping range |
| propOverlap-method | Find the proportions of an overlapping range |
| reduceMC | Reduce ranges retaining mcols |
| se | Datasets for the Fixed-Width Vignette |
| setdiffMC | Perform set operations retaining mcols |
| setdiffMC-method | Perform set operations retaining mcols |
| setoptsMC | Perform set operations retaining mcols |
| stitchRanges | Stitch Ranges within a given distance |
| unionMC | Perform set operations retaining mcols |
| unionMC-method | Perform set operations retaining mcols |
| voomWeightsFromCPM | Estimate voom precision weights directly From CPM values |