xGRviaGenomicAnnoAdv | R Documentation

## Function to conduct region-based enrichment analysis using genomic annotations via sampling

### Description

`xGRviaGenomicAnnoAdv` is supposed to conduct region-based enrichment analysis for the input genomic region data (genome build h19), using genomic annotations (eg active chromatin, transcription factor binding sites/motifs, conserved sites). Enrichment analysis is achieved by comparing the observed overlaps against the expected overlaps which are estimated from the null distribution. The null distribution is generated via sampling, that is, randomly generating samples for data genomic regions from background genomic regions. Background genomic regions can be provided by the user; by default, the annotatable genomic regions will be used.

### Usage

    xGRviaGenomicAnnoAdv(data.file, annotation.file = NULL,
    background.file = NULL, format.file = c("data.frame", "bed",
    "chr:start-end", "GRanges"), build.conversion = c(NA, "hg38.to.hg19",
    "hg18.to.hg19"), background.annotatable.only = F, num.samples = 1000,
    gap.max = 50000, max.distance = NULL, p.adjust.method = c("BH", "BY",
    "bonferroni", "holm", "hochberg", "hommel"), 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_Public_mergedTFBS",
    "ReMap_PublicAndEncode_mergedTFBS", "ReMap_Encode_TFBS",
    "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"), parallel =
    TRUE,
    multicores = NULL, verbose = T,
    RData.location = "http://galahad.well.ox.ac.uk/bigdata")

### Arguments

`data.file` | an input data file, containing a list of genomic regions to test. If the input file is formatted as a 'data.frame' (specified by the parameter 'format.file' below), the first three columns correspond to the chromosome (1st column), the starting chromosome position (2nd column), and the ending chromosome position (3rd column). If the format is indicated as 'bed' (browser extensible data), the same as 'data.frame' format but the position is 0-based offset from chromomose position. If the genomic regions provided are not ranged but only the single position, the ending chromosome position (3rd column) is allowed not to be provided. If the format is indicated as "chr:start-end", instead of using the first 3 columns, only the first column will be used and processed. If the file also contains other columns, these additional columns will be ignored. Alternatively, the input file can be the content itself assuming that input file has been read. Note: the file should use the tab delimiter as the field separator between columns.
`annotation.file` | an input annotation file containing genomic annotations for genomic regions. If the input file is formatted as a 'data.frame', the first four columns correspond to the chromosome (1st column), the starting chromosome position (2nd column), the ending chromosome position (3rd column), and the genomic annotations (eg transcription factors and histones; 4th column). If the format is indicated as 'bed', the same as 'data.frame' format but the position is 0-based offset from chromomose position. If the format is indicated as "chr:start-end", the first two columns correspond to the chromosome:start-end (1st column) and the genomic annotations (eg transcription factors and histones; 2nd column). If the file also contains other columns, these additional columns will be ignored. Alternatively, the input file can be the content itself assuming that input file has been read. Note: the file should use the tab delimiter as the field separator between columns.
`background.file` | an input background file containing a list of genomic regions as the test background. The file format is the same as 'data.file'. By default, it is NULL meaning all annotatable bases (ig non-redundant bases covered by 'annotation.file') are used as background. However, if only one annotation (eg only a transcription factor) is provided in 'annotation.file', the background must be provided.
`format.file` | the format for input files. It can be one of "data.frame", "chr:start-end", "bed" and "GRanges"
`build.conversion` | the conversion from one genome build to another. The conversions supported are "hg38.to.hg19" and "hg18.to.hg19". By default it is NA (no need to do so).
`background.annotatable.only` | logical to indicate whether the background is further restricted to annotatable bases (covered by 'annotation.file'). In other words, if the background is provided, the background bases are those after being overlapped with annotatable bases. Notably, if only one annotation (eg only a transcription factor) is provided in 'annotation.file', it should be false.
`num.samples` | the number of samples randomly generated
`gap.max` | the maximum distance of background islands to be considered away from data regions. Only background islands no far way from this distance will be considered. For example, if it is 0, meaning that only background islands that overlapp with genomic regions will be considered. By default, it is 50000
`max.distance` | the maximum distance away from data regions that is allowed when generating random samples. By default, it is NULl meaning no such restriction
`p.adjust.method` | the method used to adjust p-values. It can be one of "BH", "BY", "bonferroni", "holm", "hochberg" and "hommel". The first two methods "BH" (widely used) and "BY" control the false discovery rate (FDR: the expected proportion of false discoveries amongst the rejected hypotheses); the last four methods "bonferroni", "holm", "hochberg" and "hommel" are designed to give strong control of the family-wise error rate (FWER). Notes: FDR is a less stringent condition than FWER
`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'. Beyond pre-built annotation data, the user can specify the customised input. To do so, first save your RData file (a list of GR objects, each is an GR object correponding to an annotation) into your local computer. Then, tell "GR.annotation" with your RData file name (with or without extension), plus specify your file RData path in "RData.location". Note: you can also load your customised GR object directly
`parallel` | logical to indicate whether parallel computation with multicores is used. By default, it sets to true, but not necessarily does so. It will depend on whether these two packages "foreach" and "doParallel" have been installed. It can be installed via: `source("http://bioconductor.org/biocLite.R"); biocLite(c("foreach","doParallel"))`. If not yet installed, this option will be disabled
`multicores` | an integer to specify how many cores will be registered as the multicore parallel backend to the 'foreach' package. If NULL, it will use a half of cores available in a user's computer. This option only works when parallel computation is enabled
`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 data frame with 8 columns:

- `name`: the annotation name

- `nAnno`: the number of bases covered by that annotation. If the background is provided, they are also restricted by this

- `nOverlap`: the number of bases overlapped between input regions and annotation regions. If the background is provided, they are also restricted by this

- `fc`: fold change

- `zscore`: z-score

- `pvalue`: p-value

- `adjp`: adjusted p-value. It is the p value but after being adjusted for multiple comparisons

- `nData`: the number of bases covered by input regions

- `nBG`: the number of bases covered by background regions

### 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 (395 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_Public_mergedTFBS`: a list (131 transcription factors under GSE studies) of GenomicRanges objects; each is an GR object containing merged peaks per transcripton factor.

- `ReMap_PublicAndEncode_mergedTFBS`: a list (237 transcription factors under GSE studies and ENCODE) of GenomicRanges objects; each is an GR object containing merged peaks per transcripton factor.

- `ReMap_Encode_TFBS`: a list (155 transcription factors under 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.

### See Also

`xEnrichViewer`

### Examples

    ## Not run:
    # Load the XGR package and specify the location of built-in data
    library(XGR)
    RData.location <- "http://galahad.well.ox.ac.uk/bigdata_dev"

    # Enrichment analysis for GWAS SNPs from ImmunoBase
    ## a) provide input data
    data.file <- "http://galahad.well.ox.ac.uk/bigdata/ImmunoBase_GWAS.bed"

    ## b) perform enrichment analysis using FANTOM expressed enhancers
    eTerm <- xGRviaGenomicAnnoAdv(data.file=data.file, format.file="bed",
    GR.annotation="FANTOM5_Enhancer_Cell", num.samples=1000, gap.max=50000,
    RData.location=RData.location)

    ## c) view enrichment results for the top significant terms
    xEnrichViewer(eTerm)

    ## d) barplot of enriched terms
    bp <- xEnrichBarplot(eTerm, top_num='auto', displayBy="fdr")
    bp

    ## e) save enrichment results to the file called 'Regions_enrichments.txt'
    output <- xEnrichViewer(eTerm, top_num=length(eTerm$adjp),
    sortBy="adjp", details=TRUE)
    utils::write.table(output, file="Regions_enrichments.txt", sep="\t",
    row.names=FALSE)

    ## End(Not run)