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
|
### =========================================================================
### predictCoding methods
### =========================================================================
setMethod("predictCoding", c("Ranges", "TranscriptDb", "ANY", "DNAStringSet"),
function(query, subject, seqSource, varAllele, ..., ignore.strand=FALSE)
{
callGeneric(as(query, "GRanges"), subject, seqSource, varAllele, ...,
ignore.strand=ignore.strand)
})
setMethod("predictCoding", c("CollapsedVCF", "TranscriptDb", "ANY", "missing"),
function(query, subject, seqSource, varAllele, ..., ignore.strand=FALSE)
{
rd <- rowData(query)
alt <- alt(query)
if (is(alt, "CharacterList")) {
alt <- .toDNAStringSetList(alt)
if (sum(elementLengths(alt)) == 0L) {
stop("No nucleotide ALT values were detected.")
}
}
rd <- rep(rowData(query), elementLengths(alt))
res <- callGeneric(rd, subject, seqSource, unlist(alt, use.names=FALSE),
..., ignore.strand=ignore.strand)
## adjust QUERYID for expansion of rowData
res$QUERYID <- rep(seq_len(length(alt)),
elementLengths(alt))[res$QUERYID]
res
})
setMethod("predictCoding", c("ExpandedVCF", "TranscriptDb", "ANY", "missing"),
function(query, subject, seqSource, varAllele, ..., ignore.strand=FALSE)
{
## ExpandedVCF ALT must be DNAStringSet (CharacterList not supported)
callGeneric(rowData(query), subject, seqSource, alt(query), ...,
ignore.strand=ignore.strand)
})
setMethod("predictCoding", c("GRanges", "TranscriptDb", "ANY", "DNAStringSet"),
function(query, subject, seqSource, varAllele, ..., ignore.strand=FALSE)
{
.predictCoding(query, subject, seqSource, varAllele, ...,
ignore.strand=ignore.strand)
})
.predictCoding <-
function(query, subject, seqSource, varAllele, ...,
cache=new.env(parent=emptyenv()), ignore.strand=FALSE)
{
stopifnot(length(varAllele) == length(query))
if (!any(seqlevels(query) %in% seqlevels(subject)))
warning("none of seqlevels(query) match seqlevels(subject)")
if (!exists(".__init__", cache, inherits=FALSE)) {
cache[["cdsbytx"]] <- cdsBy(subject)
cache[["txbygene"]] <- transcriptsBy(subject, "gene")
cache[[".__init__"]] <- TRUE
}
map <- data.frame(geneid=rep(names(cache[["txbygene"]]),
elementLengths(cache[["txbygene"]])),
txid=values(unlist(cache[["txbygene"]],
use.names=FALSE))[["tx_id"]],
stringsAsFactors=FALSE)
txlocal <- .predictCodingGRangesList(query, cache[["cdsbytx"]],
seqSource, varAllele, ..., ignore.strand=ignore.strand)
txid <- values(txlocal)[["TXID"]]
values(txlocal)[["GENEID"]] <- map$geneid[match(txid, map$txid)]
txlocal
}
.predictCodingGRangesList <- function(query, cdsbytx, seqSource, varAllele,
..., genetic.code=GENETIC_CODE,
if.fuzzy.codon="error",
ignore.strand=FALSE)
{
## FIXME : set query back after olaps
if (any(insertion <- width(query) == 0))
start(query)[insertion] <- start(query)[insertion] - 1
if (ignore.strand)
strand(query) <- "*"
## retrieve local coordinates
values(query) <- append(values(query), DataFrame(varAllele=varAllele))
txlocal <- refLocsToLocalLocs(ranges=query, cdsbytx=cdsbytx)
if (length(txlocal) == 0)
return(txlocal)
rwidth <- width(txlocal)
translateidx <- rep(TRUE, length(txlocal))
## reverse complement variant alleles for "-" strand
nstrand <- as.vector(strand(txlocal) == "-")
if (any(nstrand))
values(txlocal)[["varAllele"]][nstrand] <-
reverseComplement(values(txlocal)[["varAllele"]][translateidx & nstrand])
altallele <- values(txlocal)[["varAllele"]]
fmshift <- abs(width(altallele) - rwidth) %% 3 != 0
if (any(fmshift))
translateidx[fmshift] <- FALSE
zwidth <- width(altallele) == 0
if (any(zwidth)) {
warning("records with missing 'varAllele' were ignored")
translateidx[zwidth] <- FALSE
fmshift[zwidth] <- FALSE
}
codeN <- rep(FALSE, length(txlocal))
codeN[grep("N", as.character(altallele, use.names=FALSE),
fixed=TRUE)] <-TRUE
if (any(codeN)) {
warning("varAllele values containing 'N' were not translated")
translateidx[codeN] <- FALSE
}
## reference and variant codon sequences
altpos <- (start(values(txlocal)[["CDSLOC"]]) - 1L) %% 3L + 1L
refCodon <- varCodon <- .constructRefSequences(txlocal, altpos, seqSource,
cdsbytx)
if (any(translateidx)) {
subseq(varCodon, altpos, width=rwidth)[translateidx] <-
altallele[translateidx]
## translation
refAA <- translate(refCodon, genetic.code=genetic.code,
if.fuzzy.codon=if.fuzzy.codon)
varAA <- AAStringSet(rep("", length(txlocal)))
varAA[translateidx] <- translate(varCodon[translateidx],
genetic.code=genetic.code,
if.fuzzy.codon=if.fuzzy.codon)
} else {
refAA <- varAA <- AAStringSet(rep("", length(txlocal)))
}
## results
nonsynonymous <- as.character(refAA) != as.character(varAA)
consequence <- rep("synonymous", length(txlocal))
consequence[nonsynonymous] <- "nonsynonymous"
consequence[fmshift] <- "frameshift"
consequence[nonsynonymous & (as.character(varAA) %in% "*")] <- "nonsense"
consequence[zwidth | codeN] <- "not translated"
consequence <- factor(consequence)
values(txlocal) <- append(values(txlocal),
DataFrame(GENEID=NA_character_,
CONSEQUENCE=consequence,
REFCODON=refCodon,
VARCODON=varCodon,
REFAA=refAA, VARAA=varAA))
txlocal
}
.constructRefSequences <- function(txlocal, altpos, seqSource, cdsbytx)
{
## adjust codon end for
## - width of the reference sequence
## - position of alt allele substitution in the codon
cstart <- ((start(values(txlocal)[["CDSLOC"]]) - 1L) %/% 3L) * 3L + 1L
cend <- cstart + (((altpos + width(txlocal) - 2L) %/% 3L) * 3L + 2L)
txord <- match(values(txlocal)[["TXID"]], names(cdsbytx))
txseqs <- getTranscriptSeqs(cdsbytx[txord], seqSource)
DNAStringSet(substring(txseqs, cstart, cend))
}
|
