1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
|
############################################################
#
# author: Ludwig Geistlinger
# date: 2015-03-10 13:32:37
#
# descr: get.gene.length.and.gc.content
# update: 2015-06-14 exonic sequences
############################################################
#
# @input:
# - id: one or more gene IDs (ensembl or entrez)
# - org: organism three letter code, e.g. 'hsa' for 'Homo sapiens'
# - mode: 1. biomart (supports all ensembl organisms, but might be a time-consuming)
# 2. org.db (based on BioC annotation, which is much faster but only
# for organisms with a respective TxDb, BSgenome, and OrgDb package)
getGeneLengthAndGCContent <- function(id, org, mode=c("biomart", "org.db"))
{
id.type <- .autoDetectGeneIdType(id[1])
if(is.na(id.type))
stop("Only ENTREZ or ENSEMBL gene IDs are supported.")
mode <- match.arg(mode)
inp.id <- id
# (a) based on BioC annotation utilities:
# (0) OrgDb: map between identifiers (if necessary)
# (1) TxDB: get genomic coordinates of genes
# (2) BSgenome: get sequences of genomic coordinates
#
if(mode=="org.db")
{
# check for TxDb package
txdb.pkg <- .org2pkg(org, type="TxDb")
.isAvailable(txdb.pkg, type="TxDb")
# check for BSgenome package
bsgen.pkg <- .org2pkg(org, type="BSgenome")
.isAvailable(bsgen.pkg, type="BSgenome")
txdb.spl <- unlist(strsplit(txdb.pkg, "\\."))
txdb.id.type <- txdb.spl[length(txdb.spl)]
if(txdb.id.type == "ensGene") {
txdb.id.type <- "ensembl"
} else if(txdb.id.type == "knownGene") {
txdb.id.type <- "entrez"
} else if(txdb.id.type == "sgdGene") {
txdb.id.type <- "sgd"
} else {
stop(paste("TxDb does not use ENSEMBL or ENTREZ gene IDs"))
}
# (0) map ensembl <-> entrez,
# if given id.type is entrez, but Txdb uses ensembl (or vice versa)
if(id.type != txdb.id.type)
{
orgdb.pkg <- .org2pkg(org)
.isAvailable(orgdb.pkg)
orgdb.pkg <- get(orgdb.pkg)
id.map <- mapIds(orgdb.pkg, keys=id,
column=ifelse(id.type == "entrez", "ENSEMBL", "ENTREZID"),
keytype=ifelse(id.type == "entrez", "ENTREZID", "ENSEMBL"))
id <- id.map[!is.na(id.map)]
}
# (1) get genomic coordinates
txdb.pkg <- get(txdb.pkg)
coords <- exonsBy(txdb.pkg, by="gene")
id <- id[id %in% names(coords)]
coords <- reduce(coords[id])
len <- sum(width(coords))
# (2) get sequences
bsgen.pkg <- get(bsgen.pkg)
seqs <- getSeq(bsgen.pkg, coords)
af <- alphabetFrequency(unlist(seqs, use.names=FALSE), baseOnly=TRUE, as.prob=TRUE)
gc.cont <- mean(relist(rowSums(af[,c("C", "G")]), seqs))
}
# (b) based on BioMart
#
#
else
{
id.type <- paste0(id.type, ifelse(id.type=="entrez", "gene", "_gene_id"))
# setting mart
message("Connecting to BioMart ...")
ensembl <- useMart("ENSEMBL_MART_ENSEMBL", host="www.ensembl.org")
ds <- listDatasets(ensembl)[,"dataset"]
ds <- grep(paste0("^", org), ds, value=TRUE)
if(length(ds) == 0)
stop(paste("Mart not found for:", org))
else if(length(ds) > 1)
{
message("Found several marts")
sapply(ds, function(d)
message(paste(which(ds==d), d, sep=": ")))
n <- readline(paste0("Choose mart (1-", length(ds),") : "))
ds <- ds[as.integer(n)]
}
ensembl <- useDataset(ds, mart=ensembl)
message( paste0( "Downloading sequence",
ifelse(length(id) > 1, "s", ""), " ..."))
if(length(id) > 100) message("This may take a few minutes ...")
# download sequence
# (1) get exon coordinates
attrs <- c(id.type, "ensembl_exon_id",
"chromosome_name", "exon_chrom_start", "exon_chrom_end")
coords <- getBM(filters=id.type, attributes=attrs, values=id, mart=ensembl)
id <- unique(coords[,id.type])
coords <- GRangesList(sapply(id,
function(i)
{
i.coords <- coords[coords[,1]== i, 3:5]
g <- GRanges(i.coords[,1], IRanges(i.coords[,2],i.coords[,3]))
return(g)
}), compress=FALSE)
coords <- reduce(coords)
len <- sum(width(coords))
# (2) get genes and sequences
sel <- c(id.type, "start_position", "end_position")
gene.pos <- getBM(attributes = sel, filters=id.type, values=id,
mart=ensembl)
gene.seqs <- getSequence(id=id,
type=id.type, seqType="gene_exon_intron", mart=ensembl)
# (3) get exonic sequences and correspondig GC content
gc.cont <- sapply(id,
function(i)
{
# exon coordinates, gene position & sequence for current id i
ecoords <- coords[[i]]
gpos <- gene.pos[gene.pos[,id.type] == i,
c("start_position", "end_position")]
gseq <- DNAString(
gene.seqs[gene.seqs[,id.type] == i, "gene_exon_intron"])
# exon coordinates relative to gene position
start <- start(ranges(ecoords)) - gpos[1,1] + 1
end <- end(ranges(ecoords)) - gpos[1,1] + 1
eseq <- gseq[IRanges(start, end)]
gc.cont <- sum(alphabetFrequency(eseq, as.prob=TRUE)[c("C","G")])
return(gc.cont)
}
)
}
res <- cbind(len, gc.cont)
colnames(res) <- c("length", "gc")
rownames(res) <- id
# (4) order according to input ids
if(mode == "org.db")
if(id.type != txdb.id.type)
rownames(res) <- names(id)
not.found <- !(inp.id %in% rownames(res))
na.col <- rep(NA, sum(not.found))
rn <- c(rownames(res), inp.id[not.found])
res <- rbind(res, cbind(na.col, na.col))
rownames(res) <- rn
res <- res[inp.id,]
return(res)
}
.isAvailable <- function(pkg, type="annotation")
{
if(!(pkg %in% .packages(all.available=TRUE)))
{
message(paste0("Corresponding ", type, " package not found: ",
pkg, "\nMake sure that you have it installed."))
choice <- readline("Install it now? (y/n): ")
if(choice == "y")
{
if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install(pkg)
}
else stop(paste("Package", pkg, "is not available"))
}
require(pkg, character.only = TRUE)
}
.autoDetectGeneIdType <- function(id)
{
type <- NA
if(grepl("^[Ee][Nn][Ss][A-Za-z]{0,3}[Gg][0-9]+", id)) type <- "ensembl"
else if(grepl("^[0-9]+$", id)) type <- "entrez"
else if(grepl("^[Yy][A-Za-z]{2}[0-9]{3}[A-Za-z]", id)) type <- "sgd"
else if(grepl("^[Aa][Tt][0-9][A-Za-z][0-9]{5}", id)) type <- "tair"
return(type)
}
.getOrgIdType <- function(org)
{
it <- "eg"
if(org == "At") it <- "tair"
else if(org == "Pf") it <- "plasmo"
else if(org == "Sc") it <- "sgd"
return(it)
}
.supportedOrganisms <- function() sub(".db0$", "", .availableOrgPkgs())
.availableOrgPkgs <- function(type=c("OrgDb", "TxDb", "BSgenome"), local=TRUE)
{
if(local) pkgs <- .packages(all.available=TRUE)
else pkgs <- available.packages(paste0("http://bioconductor.org/",
"packages/release/data/annotation/src/contrib"))[, "Package"]
type <- match.arg(type)
org.string <- "^org.[A-z][a-z]+.[a-z]+.db$"
if(type == "TxDb")
org.string <- "^TxDb.[A-Z][a-z]+.UCSC.[a-z]{2}[A-Za-z]*[0-9]{1,3}.[a-z]{3,5}Gene$"
else if(type == "BSgenome")
org.string <- "^BSgenome.[A-Z][a-z]+.UCSC.[a-z]{2}[A-Za-z]*[0-9]{1,3}$"
org.pkgs <- grep(org.string, pkgs, value=TRUE)
names(org.pkgs) <- NULL
return(org.pkgs)
}
.org2pkg <- function(org, type=c("OrgDb", "TxDb", "BSgenome"))
{
type <- match.arg(type)
SPECIES <- rbind(
c("anopheles", "Anopheles gambiae", "Ag", "aga", "anoGam", "7165"),
c("arabidopsis", "Arabidopsis thaliana", "At", "ath", NA, "3702"),
c("bovine", "Bos taurus", "Bt", "bta", "bosTau", "9913"),
c("canine", "Canis familiaris", "Cf", "cfa", "canFam", "9615"),
c("chicken", "Gallus gallus", "Gg", "gga", "galGal", "9031"),
c("chimp", "Pan troglodytes", "Pt", "ptr", "PanTro", "9598"),
c("ecoliK12", "Escherichia coli K12", "EcK12", "eco", NA, "562,83333,511145"),
c("ecoliSakai", "Escherichia coli Sakai", "EcSakai", "ecs", NA, "83334"),
c("fly", "Drosophila melanogaster", "Dm", "dme", "dm", "7227"),
c("human", "Homo sapiens", "Hs", "hsa", "hg", "9606"),
c("malaria", "Plasmodium falciparum", "Pf", "pfa", NA, "5833"),
c("mouse", "Mus musculus", "Mm", "mmu", "mm", "10090"),
c("pig", "Sus scrofa", "Ss", "ssc", "susScr", "9823"),
c("rat", "Rattus norvegicus", "Rn", "rno", "rn", "10116"),
c("rhesus", "Macaca mulatta", "Mmu", "mcc", "rheMac", "9544"),
c("worm", "Caenorhabditis elegans", "Ce", "cel", "ce", "6239"),
c("xenopus", "Xenopus laevis", "Xl", "xla", "NA", "8355"),
c("yeast", "Saccharomyces cerevisiae", "Sc", "sce", "sacCer", "4932,559292"),
c("zebrafish", "Danio rerio", "Dr", "dre", "danRer", "7955")
)
colnames(SPECIES) <- c("common", "tax", "bioc", "kegg", "ucsc", "ncbi")
# org specification via
# (a) 3-letter code, e.g. 'hsa'
# (b) genome assembly, e.g. 'hg38'
is.genome <- sub("[0-9]+$", "", org) %in% SPECIES[,"ucsc"]
if(is.genome)
{
ucsc.id <- org
i <- grep(sub("[0-9]+$", "", org), SPECIES[,"ucsc"])
bioc.id <- SPECIES[i, "bioc"]
}
else
{
ind <- apply(SPECIES, 1, function(r) org %in% r)
if(any(ind)) i <- which(ind)[1]
else stop(paste0("unrecognized organism ID \'", org, "\'"))
bioc.id <- SPECIES[i, "bioc"]
ucsc.id <- SPECIES[i, "ucsc"]
}
# TxDB, BSgenome, or OrgDB package?
if(type %in% c("TxDb", "BSgenome"))
{
pkg.string <- paste0("^", type, ".", bioc.id, "[a-z]+.UCSC.", ucsc.id)
pkg <- grep(pkg.string, .availableOrgPkgs(type), value=TRUE)
if(length(pkg) == 0)
pkg <- grep(pkg.string, .availableOrgPkgs(type, local=FALSE), value=TRUE)
if(length(pkg) == 0)
stop(paste("No corresponding", type, "package for", org))
else if(length(pkg) > 1)
{
message("Found several genome assemblies")
sapply(pkg, function(p)
message(paste(which(pkg==p), p, sep=": ")))
n <- readline(paste0("Choose assembly (1-", length(pkg),") : "))
pkg <- pkg[as.integer(n)]
#message("Found several genome assemblies")
#message(paste("Using latest:", pkg))
#ver <- sapply(pkg,
# function(p)
# {
# spl <- unlist(strsplit(p, "\\."))
# ind <- length(spl)
# if(type == "TxDb") ind <- ind - 1
# ass <- spl[ind]
# ver <- sub("^[a-zA-Z]+", "", ass)
# return(as.integer(ver))
# })
#pkg <- pkg[which.max(ver)]
}
}
else
{
id.type <- .getOrgIdType(bioc.id)
pkg <- paste("org", bioc.id, id.type, "db", sep=".")
}
return(pkg)
}
|
