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
|
## ----biocstyle, echo = FALSE, results = "asis", message = FALSE------------
library(BiocStyle)
BiocStyle::markdown()
## ----load-libs, message = FALSE--------------------------------------------
library(ensembldb)
library(EnsDb.Hsapiens.v86)
edbx <- filter(EnsDb.Hsapiens.v86, filter = ~ seq_name == "X")
## ----genomeToTranscript-define---------------------------------------------
gnm <- GRanges("X:107716399-107716401")
## ----genomeToTranscript-ex1-plot, message = FALSE--------------------------
library(Gviz)
## Since we're using Ensembl chromosome names we have to set:
options(ucscChromosomeNames = FALSE)
## Define a genome axis track
gat <- GenomeAxisTrack(range = gnm)
## Get all genes in that region
gnm_gns <- getGeneRegionTrackForGviz(edbx, filter = GRangesFilter(gnm))
gtx <- GeneRegionTrack(gnm_gns, name = "tx", geneSymbol = TRUE,
showId = TRUE)
## Generate a higlight track
ht <- HighlightTrack(trackList = list(gat, gtx), range = gnm)
## plot the region
plotTracks(list(ht))
## ----genomeToTranscript-ex1-map, message = FALSE---------------------------
## Map genomic coordinates to within-transcript coordinates
gnm_tx <- genomeToTranscript(gnm, edbx)
## ----genomeToTranscript-ex1-object-----------------------------------------
gnm_tx
## ----genomeToTranscript-ex2, message = FALSE-------------------------------
gnm_1 <- gnm
strand(gnm_1) <- "-"
gnm_2 <- gnm
strand(gnm_2) <- "+"
gnm <- c(gnm_1, gnm_2)
genomeToTranscript(gnm, edbx)
## ----genomeToProtein-ex1, message = FALSE----------------------------------
gnm <- GRanges("X", IRanges(start = c(630898, 644636, 644633, 634829),
width = c(5, 1, 1, 3)))
gnm_prt <- genomeToProtein(gnm, edbx)
## ----genomeToProtein-ex1-res1----------------------------------------------
gnm_prt[[1]]
## ----genomeToProtein-ex1-res2----------------------------------------------
gnm_prt[[2]]
## ----genomeToProtein-ex1-res3----------------------------------------------
gnm_prt[[3]]
## ----genomeToProtein-ex1-res3-2, message = FALSE---------------------------
prt <- proteins(edbx, filter = ProteinIdFilter(names(gnm_prt[[3]])))
nchar(prt$protein_sequence)
## ----genomeToProtein-ex1-res4----------------------------------------------
gnm_prt[[4]]
## ----proteinToTranscript-ex1, message = FALSE------------------------------
GAGE10 <- proteins(edbx, filter = ~ genename == "GAGE10")
GAGE10
## Define the IRanges object.
GAGE10_prt <- IRanges(start = 5, end = 9, names = GAGE10$protein_id)
## ----proteinToTranscript-ex1-map, message = FALSE--------------------------
GAGE10_tx <- proteinToTranscript(GAGE10_prt, edbx)
## ----proteinToTranscript-ex1-res-------------------------------------------
GAGE10_tx
## ----proteinToTranscript-ex2, message = FALSE------------------------------
ids <- c("O15266", "Q9HBJ8", "donotexistant")
prt <- IRanges(start = c(13, 43, 100), end = c(21, 80, 100))
names(prt) <- ids
prt_tx <- proteinToTranscript(prt, edbx, idType = "uniprot_id")
## ----proteinToTranscript-ex2-res1------------------------------------------
prt_tx[[1]]
## ----proteinToTranscript-ex2-res2------------------------------------------
prt_tx[[2]]
## ----proteinToTranscript-ex2-res3------------------------------------------
prt_tx[[3]]
## ----proteinToGenome-gage10-define, message = FALSE------------------------
## Define the IRanges object.
GAGE10_prt <- IRanges(start = 5, end = 9, names = "ENSP00000385415")
## ----proteinToGenome-gage10-map, message = FALSE---------------------------
GAGE10_gnm <- proteinToGenome(GAGE10_prt, edbx)
## ----proteinToGenome-gage10-res--------------------------------------------
GAGE10_gnm
## ----proteinToGenome-uniprot-ids, message = FALSE--------------------------
## Define the IRanges providing Uniprot IDs.
uni_rng <- IRanges(start = c(2, 12, 8), end = c(2, 15, 17),
names = c("D6RDZ7", "O15266", "H7C2F2"))
## We have to specify that the IDs are Uniprot IDs
uni_gnm <- proteinToGenome(uni_rng, edbx, idType = "uniprot_id")
## ----proteinToGenome-uniprot-cds_ok----------------------------------------
uni_gnm[[3]]
## ----proteinToGenome-uniprot-counts----------------------------------------
## To how many Ensembl proteins was each Uniprot ID mapped?
lengths(uni_gnm)
## ----proteinToGenome-uniprot-multi-----------------------------------------
uni_gnm[["O15266"]]
## ----proteinToGenome-SYP-fetch-domains, message = FALSE--------------------
SYP <- proteins(edbx, filter = ~ genename == "SYP",
columns = c("protein_id", "tx_id",
listColumns(edbx, "protein_domain")),
return.type = "AAStringSet")
SYP
## ----proteinToGenome-SYP-single-protein, message = FALSE-------------------
## How many proteins are annotated to SYP?
unique(mcols(SYP)$protein_id)
## Reduce the result to a single protein
SYP <- SYP[names(SYP) == "ENSP00000263233"]
## List the available protein domains and additional annotations
mcols(SYP)
## ----proteinToGenome-SYP-map, message = FALSE------------------------------
SYP_rng <- IRanges(start = mcols(SYP)$prot_dom_start,
end = mcols(SYP)$prot_dom_end)
mcols(SYP_rng) <- mcols(SYP)
## Map the domains to the genome. We set "id" to the name
## of the metadata columns containing the protein IDs
SYP_gnm <- proteinToGenome(SYP_rng, edbx, id = "protein_id")
## ----proteinToGenome-SYP-second--------------------------------------------
SYP_gnm[[2]]
## ----proteinToGenome-SYP-plot, message = FALSE-----------------------------
library(Gviz)
## Define a genome axis track
gat <- GenomeAxisTrack()
## Get the transcript ID:
txid <- SYP_gnm[[1]]$tx_id[1]
## Get a GRanges for the transcript
trt <- getGeneRegionTrackForGviz(edbx, filter = TxIdFilter(txid))
## Define a GRanges for the mapped protein domains and add
## metadata columns with the grouping of the ranges and the
## IDs of the corresponding protein domains, so they can be
## identified in the plot
dmns <- unlist(GRangesList(SYP_gnm))
dmns$grp <- rep(1:length(SYP_rng), lengths(SYP_gnm))
dmns$id <- rep(mcols(SYP_rng)$protein_domain_id, lengths(SYP_gnm))
## Since we're using Ensembl chromosome names we have to set
options(ucscChromosomeNames = FALSE)
## Plotting the transcript and the mapped protein domains.
plotTracks(list(gat,
GeneRegionTrack(trt, name = "tx"),
AnnotationTrack(dmns, group = dmns$grp,
id = dmns$id,
groupAnnotation = "id",
just.group = "above",
shape = "box",
name = "Protein domains")),
transcriptAnnotation = "transcript")
## ----transcriptToGenome-map, message = FALSE-------------------------------
rng_tx <- IRanges(start = c(501, 1), width = c(5, 5),
names = c("ENST00000486554", "ENST00000381578"))
rng_gnm <- transcriptToGenome(rng_tx, edbx)
## ----transcriptToGenome-res-1----------------------------------------------
rng_gnm
## ----pkp2-cdsToTranscript--------------------------------------------------
## Define the position within the CDS of the transcript
pkp2_cds <- IRanges(start = c(1643, 1881), width = c(1, 1),
name = rep("ENST00000070846", 2))
## Convert cds-relative to transcript-relative coordinates
pkp2 <- cdsToTranscript(pkp2_cds, EnsDb.Hsapiens.v86)
pkp2
## ----pkp2-transcriptToGenome-----------------------------------------------
pkp2_gnm <- transcriptToGenome(pkp2, EnsDb.Hsapiens.v86)
pkp2_gnm
## ----pkp2-variant-pos-validate---------------------------------------------
library(BSgenome.Hsapiens.NCBI.GRCh38)
getSeq(BSgenome.Hsapiens.NCBI.GRCh38, pkp2_gnm)
## ----transcriptToPrptein-map, message = FALSE------------------------------
rng_tx <- IRanges(start = c(501, 1, 200), width = c(5, 5, 4),
names = c("ENST00000486554", "ENST00000381578",
"ENST00000431238"))
rng_prt <- transcriptToProtein(rng_tx, edbx)
## ----transcriptToProtein-res-----------------------------------------------
rng_prt
## ----sessionInfo-----------------------------------------------------------
sessionInfo()
|
