Package index • echoannot

Annotation functions

Annotate SNPs with functional information

Brain cell-type-specific epigenomic data from Nott et al. 2019

NOTT2019_epigenomic_histograms(): Plot brain cell-specific epigenomic data
NOTT2019_get_epigenomic_peaks(): Download cell type-specific epigenomic peaks
NOTT2019_get_interactome(): Import cell type-specific interactomes
NOTT2019_get_promoter_interactome_data(): Get cell type-specific promoter/emhancer/interactome data
NOTT2019_get_regulatory_regions(): Get regulatory regions: Nott2019
NOTT2019_plac_seq_plot(): Plot brain cell-specific interactome data
get_NOTT2019_superenhancer_interactome(): Brain cell type-specific interactomes with superenhancers

Single-cell epigenomic data from Corces et al. 2020

CORCES2020_get_ATAC_peak_overlap(): Get overlap between datatable of SNPs and scATAC peaks
CORCES2020_get_hichip_fithichip_overlap(): Get overlap between data table of SNPs and HiChIP_FitHiChIP coaccessibility anchors
get_CORCES2020_bulkATACseq_peaks(): bulkATACseq peaks from human brain tissue
get_CORCES2020_cicero_coaccessibility(): Cicero_coaccessibility from human brain tissue
get_CORCES2020_hichip_fithichip_loop_calls(): FitHiChIP loop calls from human brain tissue
get_CORCES2020_scATACseq_celltype_peaks(): scATACseq cell type-specific peaks from human brain tissue
get_CORCES2020_scATACseq_peaks(): scATACseq peaks from human brain tissue

GoShifter enrichment analysis

Motif disruption analysis

Genomic region annotation via XGR

Roadmap Epigenomics chromatin state annotations

ROADMAP_construct_reference(): Gather Roadmap annotation metadata
ROADMAP_query(): Query Roadmap Query Roadmap annotations using a set of genomic coordinates.

Summary and visualization functions

CS_bin_plot(): Plot CS bin counts
CS_counts_plot(): Bar plot of tool-specific CS sizes
super_summary_plot(): Merge all summary plots into one super plot
peak_overlap_plot(): Plot overlap between some SNP group and various epigenomic data
plot_dataset_overlap(): Plot inter-study SNP overlap
plot_missense(): Plot any missense variants
convert_plots(): Convert plots to various formats
merge_celltype_specific_epigenomics(): Merge all cell-type-specific epigenomics

Helper functions

add_mb(): Add Mb
granges_overlap(): Find GenomicRanges overlap Find overlap genomic position overlap between two GRanges objects.
get_window_limits(): Get widow limits
import_ucsc_bigwigs(): Import bigwig files from the UCSC Genome Browser
test_enrichment(): Test enrichment
annotation_file_name(): Annotation file name