xDefineGenomicAnno | R Documentation

## Function to define genomic annotations

### Description

`xDefineGenomicAnno` is supposed to define genomic annotations. It returns an object of class "GenomicRangesList" (GRL).

### Usage

    xDefineGenomicAnno(GR.annotation = c(NA, "Uniform_TFBS",
    "ENCODE_TFBS_ClusteredV3", "ENCODE_TFBS_ClusteredV3_CellTypes",
    "Uniform_DNaseI_HS", "ENCODE_DNaseI_ClusteredV3",
    "ENCODE_DNaseI_ClusteredV3_CellTypes", "Broad_Histone", "SYDH_Histone",
    "UW_Histone", "FANTOM5_Enhancer_Cell", "FANTOM5_Enhancer_Tissue",
    "FANTOM5_Enhancer_Extensive", "FANTOM5_Enhancer",
    "Segment_Combined_Gm12878",
    "Segment_Combined_H1hesc", "Segment_Combined_Helas3",
    "Segment_Combined_Hepg2", "Segment_Combined_Huvec",
    "Segment_Combined_K562",
    "TFBS_Conserved", "TS_miRNA", "TCGA", "ReMap_Public_TFBS",
    "ReMap_Encode_TFBS", "ReMap_PublicAndEncode_TFBS",
    "ReMap_Public_mergedTFBS",
    "ReMap_Encode_mergedTFBS", "ReMap_PublicAndEncode_mergedTFBS",
    "Blueprint_BoneMarrow_Histone", "Blueprint_CellLine_Histone",
    "Blueprint_CordBlood_Histone", "Blueprint_Thymus_Histone",
    "Blueprint_VenousBlood_Histone", "Blueprint_DNaseI",
    "Blueprint_Methylation_hyper", "Blueprint_Methylation_hypo",
    "EpigenomeAtlas_15Segments_E029", "EpigenomeAtlas_15Segments_E030",
    "EpigenomeAtlas_15Segments_E031", "EpigenomeAtlas_15Segments_E032",
    "EpigenomeAtlas_15Segments_E033", "EpigenomeAtlas_15Segments_E034",
    "EpigenomeAtlas_15Segments_E035", "EpigenomeAtlas_15Segments_E036",
    "EpigenomeAtlas_15Segments_E037", "EpigenomeAtlas_15Segments_E038",
    "EpigenomeAtlas_15Segments_E039", "EpigenomeAtlas_15Segments_E040",
    "EpigenomeAtlas_15Segments_E041", "EpigenomeAtlas_15Segments_E042",
    "EpigenomeAtlas_15Segments_E043", "EpigenomeAtlas_15Segments_E044",
    "EpigenomeAtlas_15Segments_E045", "EpigenomeAtlas_15Segments_E046",
    "EpigenomeAtlas_15Segments_E047", "EpigenomeAtlas_15Segments_E048",
    "EpigenomeAtlas_15Segments_E050", "EpigenomeAtlas_15Segments_E051",
    "EpigenomeAtlas_15Segments_E062", "CpG_anno", "Genic_anno",
    "FANTOM5_CAT_Cell", "FANTOM5_CAT_Tissue", "FANTOM5_CAT_DO",
    "FANTOM5_CAT_EFO",
    "FANTOM5_CAT_HPO", "FANTOM5_CAT_MESH", "FANTOM5_CAT_PICS"), verbose =
    T,
    RData.location = "http://galahad.well.ox.ac.uk/bigdata")

### Arguments

`GR.annotation` | the genomic regions of annotation data. By default, it is 'NA' to disable this option. Pre-built genomic annotation data are detailed in the section 'Note'. Alternatively, the user can also directly provide a customised GR object (or a list of GR objects or a GRL object)
`verbose` | logical to indicate whether the messages will be displayed in the screen. By default, it sets to false for no display
`RData.location` | the characters to tell the location of built-in RData files. See `xRDataLoader` for details

### Value

a GRL object

### Note

The genomic annotation data are described below according to the data sources and data types.
1. ENCODE Transcription Factor ChIP-seq data

- `Uniform_TFBS`: a list (690 combinations of cell types and transcription factors) of GenomicRanges objects; each is an GR object containing uniformly identified peaks per cell type per transcription factor.

- `ENCODE_TFBS_ClusteredV3`: a list (161 transcription factors) of GenomicRanges objects; each is an GR object containing clustered peaks per transcription factor, along with a meta-column 'cells' telling cell types associtated with a clustered peak.

- `ENCODE_TFBS_ClusteredV3_CellTypes`: a list (91 cell types) of a list (transcription factors) of GenomicRanges objects. Each cell type is a list (transcription factor) of GenomicRanges objects; each is an GR object containing clustered peaks per transcription factor.

2. ENCODE DNaseI Hypersensitivity site data

- `Uniform_DNaseI_HS`: a list (125 cell types) of GenomicRanges objects; each is an GR object containing uniformly identified peaks per cell type.

- `ENCODE_DNaseI_ClusteredV3`: an GR object containing clustered peaks, along with a meta-column 'num_cells' telling how many cell types associtated with a clustered peak.

- `ENCODE_DNaseI_ClusteredV3_CellTypes`: a list (125 cell types) of GenomicRanges objects; each is an GR object containing clustered peaks per cell type.

3. ENCODE Histone Modification ChIP-seq data from different sources

- `Broad_Histone`: a list (156 combinations of cell types and histone modifications) of GenomicRanges objects; each is an GR object containing identified peaks per cell type and per histone modification. This dataset was generated from ENCODE/Broad Institute.

- `SYDH_Histone`: a list (29 combinations of cell types and histone modifications) of GenomicRanges objects; each is an GR object containing identified peaks per cell type and per histone modification. This dataset was generated from ENCODE/Stanford/Yale/Davis/Harvard.

- `UW_Histone`: a list (172 combinations of cell types and histone modifications) of GenomicRanges objects; each is an GR object containing identified peaks per cell type and per histone modification. This dataset was generated from ENCODE/University of Washington.

4. FANTOM5 expressed enhancer atlas

- `FANTOM5_Enhancer_Cell`: a list (71 cell types) of GenomicRanges objects; each is an GR object containing enhancers specifically expressed in a cell type.

- `FANTOM5_Enhancer_Tissue`: a list (41 tissues) of GenomicRanges objects; each is an GR object containing enhancers specifically expressed in a tissue.

- `FANTOM5_Enhancer_Extensive`: a list (5 categories of extensitive enhancers) of GenomicRanges objects; each is an GR object containing extensitive enhancers. They are: "Extensive_ubiquitous_enhancers_cells" for ubiquitous enhancers expressed over the entire set of cell types; "Extensive_ubiquitous_enhancers_organs" for ubiquitous enhancers expressed over the entire set of tissues; "Extensive_enhancers_tss_associations" for TSS-enhancer associations(RefSeq promoters only); "Extensive_permissive_enhancers" and "Extensive_robust_enhancers" for permissive and robust enhancer sets.

- `FANTOM5_Enhancer`: a list (117 cell types/tissues/categories) of GenomicRanges objects; each is an GR object.

5. ENCODE combined (ChromHMM and Segway) Genome Segmentation data

- `Segment_Combined_Gm12878`: a list (7 categories of segments) of GenomicRanges objects; each is an GR object containing segments per category in the cell line GM12878 (a lymphoblastoid cell line).

- `Segment_Combined_H1hesc`: a list (7 categories of segments) of GenomicRanges objects; each is an GR object containing segments per category in the cell line H1-hESC (H1 human embryonic stem cells).

- `Segment_Combined_Helas3`: a list (7 categories of segments) of GenomicRanges objects; each is an GR object containing segments per category in the cell line HeLa S3.

- `Segment_Combined_Hepg2`: a list (7 categories of segments) of GenomicRanges objects; each is an GR object containing segments per category in the cell line HepG2 (liver hepatocellular carcinoma).

- `Segment_Combined_Huvec`: a list (7 categories of segments) of GenomicRanges objects; each is an GR object containing segments per category in the cell line HUVEC (Human Umbilical Vein Endothelial Cells).

- `Segment_Combined_K562`: a list (7 categories of segments) of GenomicRanges objects; each is an GR object containing segments per category in the cell line K562 (human erythromyeloblastoid leukemia cell line).

6. Conserved TFBS

- `TFBS_Conserved`: a list (245 PWM) of GenomicRanges objects; each is an GR object containing human/mouse/rat conserved TFBS for each PWM.

7. TargetScan miRNA regulatory sites

- `TS_miRNA`: a list (153 miRNA) of GenomicRanges objects; each is an GR object containing miRNA regulatory sites for each miRNA.

8. TCGA exome mutation data

- `TCGA`: a list (11 tumor types) of GenomicRanges objects; each is an GR object containing exome mutation across tumor patients of the same tumor type.

9. ReMap integration of transcription factor ChIP-seq data (publicly available and ENCODE)

- `ReMap_Public_TFBS`: a list (1759 combinations of GSE studies and transcription factors and cell types) of GenomicRanges objects; each is an GR object containing identified peaks per GSE study per transcripton factor per cell type.

- `ReMap_Encode_TFBS`: a list (1066 combinations of ENCODE transcription factors and cell types) of GenomicRanges objects; each is an GR object containing identified peaks per ENCODE study per transcripton factor per cell type.

- `ReMap_PublicAndEncode_TFBS`: a list (2825 combinations of GSE/ENCODE studies and transcription factors and cell types) of GenomicRanges objects; each is an GR object containing identified peaks per GSE/ENCODE study per transcripton factor per cell type.

- `ReMap_Public_mergedTFBS`: a list (331 transcription factors under GSE studies) of GenomicRanges objects; each is an GR object containing merged peaks per transcripton factor.

- `ReMap_Encode_mergedTFBS`: a list (279 transcription factors under ENCODE) of GenomicRanges objects; each is an GR object containing merged peaks per transcripton factor.

- `ReMap_PublicAndEncode_mergedTFBS`: a list (485 transcription factors under GSE studies and ENCODE) of GenomicRanges objects; each is an GR object containing identified peaks per transcripton factor.

10. Blueprint Histone Modification ChIP-seq data

- `Blueprint_BoneMarrow_Histone`: a list (132 combinations of histone modifications and samples) of GenomicRanges objects; each is an GR object containing identified peaks per histone per sample (from bone marrow).

- `Blueprint_CellLine_Histone`: a list (38 combinations of histone modifications and cell lines) of GenomicRanges objects; each is an GR object containing identified peaks per histone per cell line.

- `Blueprint_CordBlood_Histone`: a list (126 combinations of histone modifications and samples) of GenomicRanges objects; each is an GR object containing identified peaks per histone per sample (from cord blood).

- `Blueprint_Thymus_Histone`: a list (5 combinations of histone modifications and samples) of GenomicRanges objects; each is an GR object containing identified peaks per histone per sample (from thymus).

- `Blueprint_VenousBlood_Histone`: a list (296 combinations of histone modifications and samples) of GenomicRanges objects; each is an GR object containing identified peaks per histone per sample (from venous blood).

11. BLUEPRINT DNaseI Hypersensitivity site data

- `Blueprint_DNaseI`: a list (36 samples) of GenomicRanges objects; each is an GR object containing identified peaks per sample.

12. BLUEPRINT DNA Methylation data

- `Blueprint_Methylation_hyper`: a list (206 samples) of GenomicRanges objects; each is an GR object containing hyper-methylated CpG regions per sample.

- `Blueprint_Methylation_hypo`: a list (206 samples) of GenomicRanges objects; each is an GR object containing hypo-methylated CpG regions per sample.

13. Roadmap Epigenomics Core 15-state Genome Segmentation data for primary cells (blood and T cells)

- `EpigenomeAtlas_15Segments_E033`: a list (15 categories of segments) of GenomicRanges objects; each is an GR object containing segments per category in the reference epigenome E033 (Primary T cells from cord blood).

- `EpigenomeAtlas_15Segments_E034`: a list (15 categories of segments) of GenomicRanges objects; each is an GR object containing segments per category in the reference epigenome E034 (Primary T cells from peripheral blood).

- `EpigenomeAtlas_15Segments_E037`: a list (15 categories of segments) of GenomicRanges objects; each is an GR object containing segments per category in the reference epigenome E037 (Primary T helper memory cells from peripheral blood 2).

- `EpigenomeAtlas_15Segments_E038`: a list (15 categories of segments) of GenomicRanges objects; each is an GR object containing segments per category in the reference epigenome E038 (Primary T helper naive cells from peripheral blood).

- `EpigenomeAtlas_15Segments_E039`: a list (15 categories of segments) of GenomicRanges objects; each is an GR object containing segments per category in the reference epigenome E039 (Primary T helper naive cells from peripheral blood).

- `EpigenomeAtlas_15Segments_E040`: a list (15 categories of segments) of GenomicRanges objects; each is an GR object containing segments per category in the reference epigenome E040 (Primary T helper memory cells from peripheral blood 1).

- `EpigenomeAtlas_15Segments_E041`: a list (15 categories of segments) of GenomicRanges objects; each is an GR object containing segments per category in the reference epigenome E041 (Primary T helper cells PMA-I stimulated).

- `EpigenomeAtlas_15Segments_E042`: a list (15 categories of segments) of GenomicRanges objects; each is an GR object containing segments per category in the reference epigenome E042 (Primary T helper 17 cells PMA-I stimulated).

- `EpigenomeAtlas_15Segments_E043`: a list (15 categories of segments) of GenomicRanges objects; each is an GR object containing segments per category in the reference epigenome E043 (Primary T helper cells from peripheral blood).

- `EpigenomeAtlas_15Segments_E044`: a list (15 categories of segments) of GenomicRanges objects; each is an GR object containing segments per category in the reference epigenome E044 (Primary T regulatory cells from peripheral blood).

- `EpigenomeAtlas_15Segments_E045`: a list (15 categories of segments) of GenomicRanges objects; each is an GR object containing segments per category in the reference epigenome E045 (Primary T cells effector/memory enriched from peripheral blood).

- `EpigenomeAtlas_15Segments_E047`: a list (15 categories of segments) of GenomicRanges objects; each is an GR object containing segments per category in the reference epigenome E047 (Primary T killer naive cells from peripheral blood).

- `EpigenomeAtlas_15Segments_E048`: a list (15 categories of segments) of GenomicRanges objects; each is an GR object containing segments per category in the reference epigenome E048 (Primary T killer memory cells from peripheral blood).

- `EpigenomeAtlas_15Segments_E062`: a list (15 categories of segments) of GenomicRanges objects; each is an GR object containing segments per category in the reference epigenome E062 (Primary mononuclear cells from peripheral blood).

14. Roadmap Epigenomics Core 15-state Genome Segmentation data for primary cells (HSC and B cells)

- `EpigenomeAtlas_15Segments_E029`: a list (15 categories of segments) of GenomicRanges objects; each is an GR object containing segments per category in the reference epigenome E029 (Primary monocytes from peripheral blood).

- `EpigenomeAtlas_15Segments_E030`: a list (15 categories of segments) of GenomicRanges objects; each is an GR object containing segments per category in the reference epigenome E030 (Primary neutrophils from peripheral blood).

- `EpigenomeAtlas_15Segments_E031`: a list (15 categories of segments) of GenomicRanges objects; each is an GR object containing segments per category in the reference epigenome E031 (Primary B cells from cord blood).

- `EpigenomeAtlas_15Segments_E032`: a list (15 categories of segments) of GenomicRanges objects; each is an GR object containing segments per category in the reference epigenome E032 (Primary B cells from peripheral blood).

- `EpigenomeAtlas_15Segments_E035`: a list (15 categories of segments) of GenomicRanges objects; each is an GR object containing segments per category in the reference epigenome E035 (Primary hematopoietic stem cells).

- `EpigenomeAtlas_15Segments_E036`: a list (15 categories of segments) of GenomicRanges objects; each is an GR object containing segments per category in the reference epigenome E036 (Primary hematopoietic stem cells short term culture).

- `EpigenomeAtlas_15Segments_E046`: a list (15 categories of segments) of GenomicRanges objects; each is an GR object containing segments per category in the reference epigenome E046 (Primary Natural Killer cells from peripheral blood).

- `EpigenomeAtlas_15Segments_E050`: a list (15 categories of segments) of GenomicRanges objects; each is an GR object containing segments per category in the reference epigenome E050 (Primary hematopoietic stem cells G-CSF-mobilized Female).

- `EpigenomeAtlas_15Segments_E051`: a list (15 categories of segments) of GenomicRanges objects; each is an GR object containing segments per category in the reference epigenome E051 (Primary hematopoietic stem cells G-CSF-mobilized Male).

15. CpG annotation

- `CpG_anno`: a list (4 categories) of GenomicRanges objects; each is an GR object. They are exclusive, including (in order) "CpG_islands", "CpG_shores" (2Kb upstream/downstream from the ends of the CpG islands), "CpG_shelves" (2Kb upstream/downstream of the farthest upstream/downstream limits of the CpG shores), and "CpG_inter" (the remaining inter-CGI genomic regions 'open sea').

16. Genic annotation

- `Genic_anno`: a list (12 categories) of GenomicRanges objects; each is an GR object. They are not exclusively, including "Genic_1to5kb" (1-5Kb upstream of TSS), "Genic_promoters" (1Kb upstream of TSS), "Genic_5UTRs", "Genic_firstexons" (first exons), "Genic_exons", "Genic_exonintronboundaries", "Genic_introns", "Genic_intronexonboundaries", "Genic_cds", "Genic_3UTRs", "Genic_intergenic" (the intergenic regions exclude the previous list of annotations), and "Genic_lncRNA" (GENCODE long non-coding RNA (lncRNA) transcripts).

17. FANTOM5 sample-ontology-enriched CAT genes

- `FANTOM5_CAT_Cell`: a list (173 cell types) of GenomicRanges objects; each is an GR object containing CAT genes specifically expressed in a cell type.

- `FANTOM5_CAT_Tissue`: a list (174 tissues) of GenomicRanges objects; each is an GR object containing CAT genes specifically expressed in a tissue.

18. FANTOM5 trait-associated CAT genes

- `FANTOM5_CAT_DO`: a list (299 traits grouped by disease ontology) of GenomicRanges objects; each is an GR object containing CAT genes harboring at least one trait-associated SNP.

- `FANTOM5_CAT_EFO`: a list (93 traits grouped by experiment factor ontology) of GenomicRanges objects; each is an GR object containing CAT genes harboring at least one trait-associated SNP.

- `FANTOM5_CAT_HPO`: a list (176 traits grouped by human phenotype ontology) of GenomicRanges objects; each is an GR object containing CAT genes harboring at least one trait-associated SNP.

- `FANTOM5_CAT_MESH`: a list (210 traits grouped by Medical Subject Headings) of GenomicRanges objects; each is an GR object containing CAT genes harboring at least one trait-associated SNP.

- `FANTOM5_CAT_PICS`: a list (39 traits grouped by PICS dieases) of GenomicRanges objects; each is an GR object containing CAT genes harboring at least one trait-associated SNP.

19. GWAS Catalog trait-associated SNPs

- `GWAScatalog_alltraits`: a list (390 traits grouped by EFO) of GenomicRanges objects; each is an GR object containing trait-associated SNPs.

- `GWAScatalog_bloodindex`: a list (29 traits grouped by EFO) of GenomicRanges objects; each is an GR object containing trait-associated SNPs.

### See Also

`xEnrichViewer`

### Examples

    # Load the XGR package and specify the location of built-in data
    library(XGR)
    RData.location <- "http://galahad.well.ox.ac.uk/bigdata"

    ## Not run:
    grl <- xDefineGenomicAnno("Uniform_TFBS",
    RData.location=RData.location)
    grl <- xDefineGenomicAnno("Uniform_DNaseI_HS",
    RData.location=RData.location)
    grl <- xDefineGenomicAnno("FANTOM5_Enhancer_Cell",
    RData.location=RData.location)
    grl <- xDefineGenomicAnno("ReMap_Public_TFBS",
    RData.location=RData.location)
    grl <- xDefineGenomicAnno("EpigenomeAtlas_15Segments_E029",
    RData.location=RData.location)
    grl <- xDefineGenomicAnno("FANTOM5_CAT_Cell",
    RData.location=RData.location)
    grl <- xDefineGenomicAnno("GWAScatalog_alltraits",
    RData.location=RData.location)

    # the customised
    ## a GR object
    GR.annotation <- grl[[1]]
    grl_customised <- xDefineGenomicAnno(GR.annotation,
    RData.location=RData.location)
    ## a list of GR objects
    GR.annotation <- lapply(grl[1:2], function(x) x)
    grl_customised <- xDefineGenomicAnno(GR.annotation,
    RData.location=RData.location)

    ## End(Not run)