1+ # ' @include union.R
2+ NULL
3+
4+ # ' Add meta data column to anchors based on .bed file
5+ # '
6+ # ' \code{annotateAnchors} adds a logical variable to meta data columns in the
7+ # ' anchors based on a GRanges object of features' genomic coordinates
8+ # '
9+ # ' This function adds column of TRUE/FALSE values on the loopdata object
10+ # ' anchors whether a feature is observed nearby in \code{features}. The name
11+ # ' of this column that will be in the anchors GRanges object is specified by
12+ # ' a user defined string \code{featureName}. Gap tolerance between a feature
13+ # ' and an anchor is specified by \code{maxgap}, where the default is 1,000bp.
14+ # '
15+ # ' @param dlo A loopdata object whose anchors will be annotated
16+ # ' @param features A Granges object corresponding to locations of interest
17+ # ' @param featureName A string that will be the mcol name in anchors
18+ # ' @param maxgap A value of max permissible gap between a feature and anchor
19+ # '
20+ # ' @return A loopdata object with new meta data column in anchors
21+ # '
22+ # ' @examples
23+ # ' # Annotate whether anchors are near a gene body; within 1kb
24+ # ' rda<-paste(system.file('rda',package='diffloop'),'jpn_chr1reg.rda',sep='/')
25+ # ' load(rda)
26+ # ' gb <-getHumanGenes()
27+ # ' jpn_chr1reg <- annotateAnchors(jpn_chr1reg,gb,'nearGeneBody')
28+ # '
29+ # ' # Adding close to gene bodies with no gap tolerance
30+ # ' jpn_chr1reg <- annotateAnchors(jpn_chr1reg,gb,'inGeneBody',0)
31+ # '
32+ # ' @import GenomicRanges
33+ # '
34+ # ' @export
35+ setGeneric (name = "annotateAnchors ", def = function(dlo, features,
36+ featureName , maxgap ) standardGeneric(" annotateAnchors"
37+
38+ .annotateAnchors <- function (dlo , features , featureName , maxgap ) {
39+ hits <- suppressWarnings(findOverlaps(features , dlo @ anchors ,
40+ maxgap = maxgap ))
41+ idx <- unique(subjectHits(hits ))
42+ values <- data.frame (matrix (FALSE , ncol = 1 , nrow = length(ranges(dlo @ anchors ))))
43+ values [idx , ] <- TRUE
44+ colnames(values ) <- featureName
45+ mcols(dlo @ anchors ) <- c(mcols(dlo @ anchors ), values )
46+ return (dlo )
47+ }
48+
49+ # ' @rdname annotateAnchors
50+ setMethod (f = "annotateAnchors ", signature = c("loopdata", "GRanges",
51+ " character" " missing" definition = function (dlo , features ,
52+ featureName , maxgap = 1000 ) {
53+ maxgap <- 1000
54+ .annotateAnchors(dlo , features , featureName , maxgap )
55+ })
56+
57+ # ' @rdname annotateAnchors
58+ setMethod (f = "annotateAnchors ", signature = c("loopdata", "GRanges",
59+ " character" " numeric" definition = function (dlo , features ,
60+ featureName , maxgap ) {
61+ .annotateAnchors(dlo , features , featureName , maxgap )
62+ })
63+
64+
65+ # ' Get protein coding gene regions
66+ # '
67+ # ' \code{getHumanGenes} returns a \code{GRanges} object of all protein
68+ # ' coding genes genome-wide or within specified chromosomes
69+ # '
70+ # ' This function returns a \code{GRanges} object with the coordinates and
71+ # ' gene IDs of all protein coding genes either genome-wide
72+ # ' (by default) orspecified within a particular chromosome.
73+ # '
74+ # ' @param chr A vector of chromosomes
75+ # '
76+ # ' @return A GRanges object
77+ # '
78+ # ' @examples
79+ # ' # Grab all protein coding gene locations genome-wide
80+ # ' pc.genes <- getHumanGenes()
81+ # ' # Grab all protein coding gene loctions on chromosome 1
82+ # ' chr1 <- getHumanGenes(c('1'))
83+ # ' @import GenomicRanges
84+ # ' @import biomaRt
85+ # ' @importFrom GenomeInfoDb sortSeqlevels seqlevels seqlevels<-
86+ # ' @importFrom S4Vectors queryHits subjectHits
87+ # '
88+ # ' @export
89+ setGeneric (name = "getHumanGenes ", def = function(chr) standardGeneric("getHumanGenes"))
90+
91+ # ' @import GenomicRanges
92+ .getHumanGenes <- function (chr ) {
93+ vals = list (chr , " protein_coding"
94+ mart = useMart(biomart = " ensembl" dataset = " hsapiens_gene_ensembl"
95+ geneinfo = getBM(attributes = c(" chromosome_name" " start_position"
96+ " end_position" " external_gene_name" filters = c(" chromosome_name"
97+ " biotype" values = vals , mart = mart )
98+ colnames(geneinfo ) <- c(" chr" " start" " end" " id"
99+ raw <- makeGRangesFromDataFrame(geneinfo , keep.extra.columns = TRUE ,
100+ ignore.strand = TRUE , seqnames.field = c(" chr" start.field = " start"
101+ end.field = c(" end" starts.in.df.are.0based = FALSE )
102+ gr <- sortSeqlevels(raw )
103+ gr <- sort(gr )
104+ return (gr )
105+ }
106+
107+ # ' @rdname getHumanGenes
108+ setMethod (f = "getHumanGenes ", signature = c("missing"), definition = function(chr) {
109+ all <- c(" 1" " 2" " 3" " 4" " 5" " 6" " 7" " 8" " 9" " 10"
110+ " 11" " 12" " 13" " 14" " 15" " 16" " 17" " 18" " 19"
111+ " 20" " 21" " 22" " X" " Y"
112+ return (.getHumanGenes(all ))
113+ })
114+
115+ # ' @rdname getHumanGenes
116+ setMethod (f = "getHumanGenes ", signature = c("character"), definition = function(chr) {
117+ return (.getHumanGenes(chr ))
118+ })
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