Nothing
R/annotation.R
In SGSeq: Splice event prediction and quantification from RNA-seq data
Defines functions
matchSplice
matchExon
matchJunction
matchSGFeatures
matchTxFeatures
annotatePaths
annotateSegments
propagateAnnotation
annotateFeatures
addDummySpliceSites
annotate
Documented in
annotate
##' Features in \code{query} are assigned transcript names and gene names
##' of structurally compatible features in \code{subject} (see below).
##' If a feature in \code{query} does not match any features in
##' \code{subject}, its geneName inherits from connected annotated features.
##'
##' Feature matching is performed as follows:
##' Query splice junctions are matched with identical subject splice
##' junctions. Query splice sites are matched with splice sites
##' implied by subject splice junctions. Query exon bins are matched with
##' overlapping subject exons. Spliced boundaries of query exon bins
##' must match spliced subject exon boundaries. Query exon bins cannot
##' extend across spliced subject exon boundaries.
##'
##' @title Annotation with respect to transcript features
##' @param query \code{SGFeatures}, \code{SGVariants},
##' \code{SGFeatureCounts} or \code{SGVariantCounts} object
##' @param subject \code{TxFeatures} object
##' @return \code{query} with updated \code{txName}, \code{geneName}
##' column slots
##' @examples
##' sgf_annotated <- annotate(sgf_pred, txf_ann)
##' sgv_annotated <- annotate(sgv_pred, txf_ann)
##' @author Leonard Goldstein
annotate <- function(query, subject)
{
if (!is(subject, "TxFeatures")) {
stop("subject must be a TxFeatures object")
}
if (is(query, "SGFeatures")) {
query <- annotateFeatures(query, subject)
} else if (is(query, "SGVariants")) {
query <- updateObject(query, verbose = TRUE)
query_class <- class(query)
query_mcols <- mcols(query)
query_unlisted <- unlist(query, use.names = FALSE)
extended <- addDummySpliceSites(query_unlisted)
extended <- annotate(extended, subject)
i <- match(featureID(query_unlisted), featureID(extended))
query_unlisted <- extended[i]
query <- relist(query_unlisted, query)
mcols(query) <- query_mcols
query <- new(query_class, query)
query <- annotatePaths(query)
} else if (is(query, "Counts")) {
rd <- rowRanges(query)
rd <- annotate(rd, subject)
rowRanges(query) <- rd
}
return(query)
}
addDummySpliceSites <- function(features)
{
junctions <- features[type(features) == "J"]
for (type in c("D", "A")) {
S <- flank(junctions, -1, switch(type, "D" = TRUE, "A" = FALSE))
S <- granges(S)
i <- which(!duplicated(S))
S <- S[i]
mcols(S)$type <- rep(type, length(i))
mcols(S)$splice5p <- rep(NA, length(i))
mcols(S)$splice3p <- rep(NA, length(i))
mcols(S)$featureID <- seq_along(i) + max(featureID(features))
mcols(S)$geneID <- geneID(junctions)[i]
S <- SGFeatures(S)
new2old <- match(seqlevels(features), seqlevels(S))
seqinfo(S, new2old = new2old) <- seqinfo(features)
features <- c(features, S)
}
return(features)
}
annotateFeatures <- function(query, subject)
{
i <- which(type(subject) %in% c("F", "L"))
if (length(i) > 0) {
subject <- c(subject[-i], mergeExonsTerminal(subject[i], 1))
}
if (is(query, "TxFeatures")) {
hits <- matchTxFeatures(query, subject)
} else if (is(query, "SGFeatures")) {
hits <- matchSGFeatures(query, subject)
}
qH <- queryHits(hits)
sH <- subjectHits(hits)
for (option in c("tx", "gene")) {
q_id <- factor(slot(query, "featureID"))
s_ann <- slot(subject, paste0(option, "Name"))
id_ann <- splitCharacterList(s_ann[sH], q_id[qH])
q_ann <- setNames(id_ann[match(q_id, names(id_ann))], NULL)
slot(query, paste0(option, "Name")) <- q_ann
}
if (is(query, "SGFeatures")) {
query <- propagateAnnotation(query)
}
return(query)
}
propagateAnnotation <- function(query)
{
## select partially annotated components
query_ann <- elementNROWS(geneName(query)) > 0
gid <- intersect(geneID(query)[query_ann], geneID(query)[!query_ann])
if (length(gid) == 0) return(query)
g <- spliceGraph(query[geneID(query) %in% gid])
## remove uninformative edges
## (annotated edges with annotated 'from' and 'to' nodes)
gv <- nodes(g)
gd <- edges(g)
gd$from <- match(gd$from, gv$name)
gd$to <- match(gd$to, gv$name)
gd_ann <- elementNROWS(gd$geneName) > 0
fr_ann <- query_ann[match(gv$featureID[gd$from], featureID(query))]
to_ann <- query_ann[match(gv$featureID[gd$to], featureID(query))]
excl <- which(gd_ann & (fr_ann | is.na(fr_ann)) & (to_ann | is.na(to_ann)))
if (length(excl) > 0) g <- delete.edges(g, excl)
## remove uninformative nodes (unconnected nodes)
excl <- which(degree(g, mode = "in") == 0 & degree(g, mode = "out") == 0)
if (length(excl) > 0) g <- delete.vertices(g, excl)
## graph information
gv <- nodes(g)
gd <- edges(g)
gd$from <- match(gd$from, gv$name)
gd$to <- match(gd$to, gv$name)
gv$geneName <- lapply(vector("list", nrow(gv)), as.character)
i <- which(!is.na(gv$featureID))
gv$geneName[i] <- as.list(geneName(query))[
match(gv$featureID[i], featureID(query))]
gv$cluster <- clusters(g)$membership
gd$cluster <- gv$cluster[gd$from]
cluster2geneName <- splitCharacterList(
c(gv$geneName, gd$geneName), factor(c(gv$cluster, gd$cluster)))
cluster2geneName <- cluster2geneName[elementNROWS(cluster2geneName) == 1]
## select unannotated features
i_gd <- which(elementNROWS(gd$geneName) == 0)
i_gv <- which(elementNROWS(gv$geneName) == 0 & !is.na(gv$featureID))
fid <- c(gd$featureID[i_gd], gv$featureID[i_gv])
n_1 <- c(gd$from[i_gd], i_gv)
n_2 <- c(gd$to[i_gd], i_gv)
cluster <- gv$cluster[n_1]
## unannotated features inherit gene names from connected features
ann <- CharacterList(vector("list", length(fid)))
i <- which(as.character(cluster) %in% names(cluster2geneName))
ann[i] <- cluster2geneName[match(cluster[i], names(cluster2geneName))]
i <- which(!as.character(cluster) %in% names(cluster2geneName))
bwd <- lapply(n_1[i], function(x) {
v <- subcomponent(g, x, "in")
d <- which(gd$to %in% v)
sort(unique(unlist(c(gv$geneName[v], gd$geneName[d])))) })
fwd <- lapply(n_2[i], function(x) {
v <- subcomponent(g, x, "out")
d <- which(gd$from %in% v)
sort(unique(unlist(c(gv$geneName[v], gd$geneName[d])))) })
w <- pintersect(bwd, fwd)
j <- which(elementNROWS(w) == 0)
w[j] <- punion(bwd[j], fwd[j])
ann[i] <- CharacterList(w)
## update query geneName column
geneName(query)[match(fid, featureID(query))] <- ann
return(query)
}
annotateSegments <- function(ids, features)
{
out <- vector("list", length(ids))
segment_ids <- strsplit(ids, ",")
segment_n <- elementNROWS(segment_ids)
ids <- unlist(segment_ids)
ids_segment <- togroup0(segment_ids)
ids_ann <- vector("list", length(ids))
ids_ann <- as(ids_ann, "CharacterList")
i <- grep("^\\d+$", ids)
if (length(i) > 0) {
ids_ann[i] <- txName(features)[match(ids[i], featureID(features))]
}
i <- grep("^\\{\\S*\\}$", ids)
if (length(i) > 0) {
tmp <- ids[i]
tmp <- gsub("\\{|\\}", "", tmp)
tmp <- strsplit(tmp, ";", fixed = TRUE)
tmp <- as(tmp, "CharacterList")
ids_ann[i] <- tmp
}
ann <- unlist(ids_ann)
ann_id <- togroup0(ids_ann)
ann_segment <- ids_segment[ann_id]
if (length(ann) == 0) {
return(out)
}
segment_ann_n <- table(paste0(ann_segment, ":", ann))
x_segment <- vapply(strsplit(names(segment_ann_n), ":"),
"[", character(1), 1)
x_ann <- sub("^\\d+:", "", names(segment_ann_n))
i <- which(segment_ann_n == segment_n[as.integer(x_segment)])
if (length(i) > 0) {
x_segment <- x_segment[i]
x_ann <- x_ann[i]
segment_ann <- split(x_ann, x_segment)
out[as.integer(names(segment_ann))] <- segment_ann
}
return(out)
}
annotatePaths <- function(paths)
{
features <- unlist(paths)
## encode txName
txName_unique <- unique(unlist(txName(features)))
txName(features) <- relist(as.character(match(unlist(txName(features)),
txName_unique)), txName(features))
x <- featureID(paths)
i <- grep("(", x, fixed = TRUE)
while (length(i) > 0) {
## find inner event
m <- regexpr("\\([^\\(\\)]+\\)", x[i])
l <- attr(m, "match.length")
## split at event
u <- substr(x[i], 1, m - 1)
b <- substr(x[i], m + 1, m + l - 2)
v <- substr(x[i], m + l, nchar(x)[i])
## annotate event
list_ids <- strsplit(b, "|", fixed = TRUE)
ids <- unlist(list_ids)
ids_path <- i[togroup0(list_ids)]
ids_ann <- annotateSegments(ids, features)
ann <- unlist(ids_ann)
ann_id <- togroup0(ids_ann)
ann_path <- ids_path[ann_id]
path_ann <- vector("list", length(i))
if (!is.null(ann)) {
tmp <- tapply(ann, ann_path, unique, simplify = FALSE)
path_ann[match(names(tmp), i)] <- tmp
}
path_ann <- paste0("{", unstrsplit(path_ann, ";"), "}")
x[i] <- paste0(u, path_ann, v)
i <- grep("(", x, fixed = TRUE)
}
out <- annotateSegments(x, features)
out <- as(out, "CharacterList")
## decode txName
out <- relist(txName_unique[as.integer(unlist(out))], out)
txName(paths) <- out
## geneName
path_ids <- extractIDs(featureID(paths))
path_ids_unlisted <- unlist(path_ids)
i <- match(path_ids_unlisted, featureID(features))
f <- factor(togroup0(path_ids), levels = seq_along(path_ids))
path_ann <- splitCharacterList(geneName(features)[i], f)
geneName(paths) <- setNames(path_ann, NULL)
return(paths)
}
matchTxFeatures <- function(query, subject)
{
q <- feature2name(query, TRUE)
s <- feature2name(subject, TRUE)
s2i <- split(seq_along(s), s)
qH <- which(q %in% names(s2i))
sH <- match(q[qH], names(s2i))
qH <- qH[togroup0(sH)]
sH <- unlist(sH)
Hits(qH, sH, length(query), length(subject),
sort.by.query = TRUE)
}
matchSGFeatures <- function(query, subject) {
Reduce(union, list(
matchJunction(query, subject),
matchExon(query, subject),
matchSplice(query, subject, "D"),
matchSplice(query, subject, "A")
))
}
matchJunction <- function(query, subject) {
i_q <- which(type(query) == "J")
i_s <- which(type(subject) == "J")
hits <- findMatches(query[i_q], subject[i_s])
qH <- queryHits(hits)
sH <- subjectHits(hits)
Hits(i_q[qH], i_s[sH], length(query), length(subject),
sort.by.query = TRUE)
}
matchExon <- function(query, subject, stringent = TRUE) {
i_q <- which(type(query) == "E")
i_s <- which(type(subject) %in% c("I", "F", "L", "U"))
q2 <- query[i_q]
s2 <- subject[i_s]
hits <- findOverlaps(q2, s2)
qH <- queryHits(hits)
sH <- subjectHits(hits)
hits <- Hits(i_q[qH], i_s[sH], length(query), length(subject),
sort.by.query = TRUE)
if (!stringent) { return(hits) }
## exclude hits with inconsistent 5' spliced boundary
i <- which(splice5p(q2)[qH])
if (length(i) > 0) {
q2_5p <- start(flank(q2[qH][i], -1, TRUE))
s2_5p <- start(flank(s2[sH][i], -1, TRUE))
s2_type <- type(s2)[sH][i]
excl_q_5p <- i[which(q2_5p != s2_5p | s2_type %in% c("F", "U"))]
} else { excl_q_5p <- integer() }
## exclude hits with inconsistent 3' spliced boundary
i <- which(splice3p(q2)[qH])
if (length(i) > 0) {
q2_3p <- start(flank(q2[qH][i], -1, FALSE))
s2_3p <- start(flank(s2[sH][i], -1, FALSE))
s2_type <- type(s2)[sH][i]
excl_q_3p <- i[which(q2_3p != s2_3p | s2_type %in% c("L", "U"))]
} else { excl_q_3p <- integer() }
## exclude hits with query overlapping 5' flanking intron
i <- which(type(s2)[sH] %in% c("I", "L"))
if (length(i) > 0) {
hits_2 <- findOverlaps(q2[qH][i], flank(s2[sH][i], 1, TRUE))
hits_2 <- hits_2[queryHits(hits_2) == subjectHits(hits_2)]
excl_s_5p <- i[queryHits(hits_2)]
} else { excl_s_5p <- integer() }
## exclude hits with query overlapping 3' flanking intron
i <- which(type(s2)[sH] %in% c("F", "I"))
if (length(i) > 0) {
hits_2 <- findOverlaps(q2[qH][i], flank(s2[sH][i], 1, FALSE))
hits_2 <- hits_2[queryHits(hits_2) == subjectHits(hits_2)]
excl_s_3p <- i[queryHits(hits_2)]
} else { excl_s_3p <- integer() }
excl <- unique(c(excl_q_5p, excl_q_3p, excl_s_5p, excl_s_3p))
if (length(excl) > 0) { hits <- hits[-excl] }
return(hits)
}
matchSplice <- function(query, subject, type = c("D", "A")) {
type <- match.arg(type)
i_q <- which(type(query) == type)
q <- query[i_q]
if (type == "D") {
i_s_J <- which(type(subject) == "J")
s_J <- flank(subject[i_s_J], -1, TRUE)
i_s_E <- which(type(subject) %in% c("I", "F"))
s_E <- flank(subject[i_s_E], -1, FALSE)
} else if (type == "A") {
i_s_J <- which(type(subject) == "J")
s_J <- flank(subject[i_s_J], -1, FALSE)
i_s_E <- which(type(subject) %in% c("I", "L"))
s_E <- flank(subject[i_s_E], -1, TRUE)
}
i_s <- c(i_s_J, i_s_E)
s <- c(s_J, s_E)
hits <- findMatches(q, s)
qH <- queryHits(hits)
sH <- subjectHits(hits)
Hits(i_q[qH], i_s[sH], length(query), length(subject),
sort.by.query = TRUE)
}
Try the SGSeq package in your browser
Any scripts or data that you put into this service are public.
SGSeq documentation built on Nov. 8, 2020, 8:31 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions matchSplice matchExon matchJunction matchSGFeatures matchTxFeatures annotatePaths annotateSegments propagateAnnotation annotateFeatures addDummySpliceSites annotate
Documented in annotate
##' Features in \code{query} are assigned transcript names and gene names
##' of structurally compatible features in \code{subject} (see below).
##' If a feature in \code{query} does not match any features in
##' \code{subject}, its geneName inherits from connected annotated features.
##'
##' Feature matching is performed as follows:
##' Query splice junctions are matched with identical subject splice
##' junctions. Query splice sites are matched with splice sites
##' implied by subject splice junctions. Query exon bins are matched with
##' overlapping subject exons. Spliced boundaries of query exon bins
##' must match spliced subject exon boundaries. Query exon bins cannot
##' extend across spliced subject exon boundaries.
##'
##' @title Annotation with respect to transcript features
##' @param query \code{SGFeatures}, \code{SGVariants},
##' \code{SGFeatureCounts} or \code{SGVariantCounts} object
##' @param subject \code{TxFeatures} object
##' @return \code{query} with updated \code{txName}, \code{geneName}
##' column slots
##' @examples
##' sgf_annotated <- annotate(sgf_pred, txf_ann)
##' sgv_annotated <- annotate(sgv_pred, txf_ann)
##' @author Leonard Goldstein
annotate <- function(query, subject)
{
if (!is(subject, "TxFeatures")) {
stop("subject must be a TxFeatures object")
}
if (is(query, "SGFeatures")) {
query <- annotateFeatures(query, subject)
} else if (is(query, "SGVariants")) {
query <- updateObject(query, verbose = TRUE)
query_class <- class(query)
query_mcols <- mcols(query)
query_unlisted <- unlist(query, use.names = FALSE)
extended <- addDummySpliceSites(query_unlisted)
extended <- annotate(extended, subject)
i <- match(featureID(query_unlisted), featureID(extended))
query_unlisted <- extended[i]
query <- relist(query_unlisted, query)
mcols(query) <- query_mcols
query <- new(query_class, query)
query <- annotatePaths(query)
} else if (is(query, "Counts")) {
rd <- rowRanges(query)
rd <- annotate(rd, subject)
rowRanges(query) <- rd
}
return(query)
}
addDummySpliceSites <- function(features)
{
junctions <- features[type(features) == "J"]
for (type in c("D", "A")) {
S <- flank(junctions, -1, switch(type, "D" = TRUE, "A" = FALSE))
S <- granges(S)
i <- which(!duplicated(S))
S <- S[i]
mcols(S)$type <- rep(type, length(i))
mcols(S)$splice5p <- rep(NA, length(i))
mcols(S)$splice3p <- rep(NA, length(i))
mcols(S)$featureID <- seq_along(i) + max(featureID(features))
mcols(S)$geneID <- geneID(junctions)[i]
S <- SGFeatures(S)
new2old <- match(seqlevels(features), seqlevels(S))
seqinfo(S, new2old = new2old) <- seqinfo(features)
features <- c(features, S)
}
return(features)
}
annotateFeatures <- function(query, subject)
{
i <- which(type(subject) %in% c("F", "L"))
if (length(i) > 0) {
subject <- c(subject[-i], mergeExonsTerminal(subject[i], 1))
}
if (is(query, "TxFeatures")) {
hits <- matchTxFeatures(query, subject)
} else if (is(query, "SGFeatures")) {
hits <- matchSGFeatures(query, subject)
}
qH <- queryHits(hits)
sH <- subjectHits(hits)
for (option in c("tx", "gene")) {
q_id <- factor(slot(query, "featureID"))
s_ann <- slot(subject, paste0(option, "Name"))
id_ann <- splitCharacterList(s_ann[sH], q_id[qH])
q_ann <- setNames(id_ann[match(q_id, names(id_ann))], NULL)
slot(query, paste0(option, "Name")) <- q_ann
}
if (is(query, "SGFeatures")) {
query <- propagateAnnotation(query)
}
return(query)
}
propagateAnnotation <- function(query)
{
## select partially annotated components
query_ann <- elementNROWS(geneName(query)) > 0
gid <- intersect(geneID(query)[query_ann], geneID(query)[!query_ann])
if (length(gid) == 0) return(query)
g <- spliceGraph(query[geneID(query) %in% gid])
## remove uninformative edges
## (annotated edges with annotated 'from' and 'to' nodes)
gv <- nodes(g)
gd <- edges(g)
gd$from <- match(gd$from, gv$name)
gd$to <- match(gd$to, gv$name)
gd_ann <- elementNROWS(gd$geneName) > 0
fr_ann <- query_ann[match(gv$featureID[gd$from], featureID(query))]
to_ann <- query_ann[match(gv$featureID[gd$to], featureID(query))]
excl <- which(gd_ann & (fr_ann | is.na(fr_ann)) & (to_ann | is.na(to_ann)))
if (length(excl) > 0) g <- delete.edges(g, excl)
## remove uninformative nodes (unconnected nodes)
excl <- which(degree(g, mode = "in") == 0 & degree(g, mode = "out") == 0)
if (length(excl) > 0) g <- delete.vertices(g, excl)
## graph information
gv <- nodes(g)
gd <- edges(g)
gd$from <- match(gd$from, gv$name)
gd$to <- match(gd$to, gv$name)
gv$geneName <- lapply(vector("list", nrow(gv)), as.character)
i <- which(!is.na(gv$featureID))
gv$geneName[i] <- as.list(geneName(query))[
match(gv$featureID[i], featureID(query))]
gv$cluster <- clusters(g)$membership
gd$cluster <- gv$cluster[gd$from]
cluster2geneName <- splitCharacterList(
c(gv$geneName, gd$geneName), factor(c(gv$cluster, gd$cluster)))
cluster2geneName <- cluster2geneName[elementNROWS(cluster2geneName) == 1]
## select unannotated features
i_gd <- which(elementNROWS(gd$geneName) == 0)
i_gv <- which(elementNROWS(gv$geneName) == 0 & !is.na(gv$featureID))
fid <- c(gd$featureID[i_gd], gv$featureID[i_gv])
n_1 <- c(gd$from[i_gd], i_gv)
n_2 <- c(gd$to[i_gd], i_gv)
cluster <- gv$cluster[n_1]
## unannotated features inherit gene names from connected features
ann <- CharacterList(vector("list", length(fid)))
i <- which(as.character(cluster) %in% names(cluster2geneName))
ann[i] <- cluster2geneName[match(cluster[i], names(cluster2geneName))]
i <- which(!as.character(cluster) %in% names(cluster2geneName))
bwd <- lapply(n_1[i], function(x) {
v <- subcomponent(g, x, "in")
d <- which(gd$to %in% v)
sort(unique(unlist(c(gv$geneName[v], gd$geneName[d])))) })
fwd <- lapply(n_2[i], function(x) {
v <- subcomponent(g, x, "out")
d <- which(gd$from %in% v)
sort(unique(unlist(c(gv$geneName[v], gd$geneName[d])))) })
w <- pintersect(bwd, fwd)
j <- which(elementNROWS(w) == 0)
w[j] <- punion(bwd[j], fwd[j])
ann[i] <- CharacterList(w)
## update query geneName column
geneName(query)[match(fid, featureID(query))] <- ann
return(query)
}
annotateSegments <- function(ids, features)
{
out <- vector("list", length(ids))
segment_ids <- strsplit(ids, ",")
segment_n <- elementNROWS(segment_ids)
ids <- unlist(segment_ids)
ids_segment <- togroup0(segment_ids)
ids_ann <- vector("list", length(ids))
ids_ann <- as(ids_ann, "CharacterList")
i <- grep("^\\d+$", ids)
if (length(i) > 0) {
ids_ann[i] <- txName(features)[match(ids[i], featureID(features))]
}
i <- grep("^\\{\\S*\\}$", ids)
if (length(i) > 0) {
tmp <- ids[i]
tmp <- gsub("\\{|\\}", "", tmp)
tmp <- strsplit(tmp, ";", fixed = TRUE)
tmp <- as(tmp, "CharacterList")
ids_ann[i] <- tmp
}
ann <- unlist(ids_ann)
ann_id <- togroup0(ids_ann)
ann_segment <- ids_segment[ann_id]
if (length(ann) == 0) {
return(out)
}
segment_ann_n <- table(paste0(ann_segment, ":", ann))
x_segment <- vapply(strsplit(names(segment_ann_n), ":"),
"[", character(1), 1)
x_ann <- sub("^\\d+:", "", names(segment_ann_n))
i <- which(segment_ann_n == segment_n[as.integer(x_segment)])
if (length(i) > 0) {
x_segment <- x_segment[i]
x_ann <- x_ann[i]
segment_ann <- split(x_ann, x_segment)
out[as.integer(names(segment_ann))] <- segment_ann
}
return(out)
}
annotatePaths <- function(paths)
{
features <- unlist(paths)
## encode txName
txName_unique <- unique(unlist(txName(features)))
txName(features) <- relist(as.character(match(unlist(txName(features)),
txName_unique)), txName(features))
x <- featureID(paths)
i <- grep("(", x, fixed = TRUE)
while (length(i) > 0) {
## find inner event
m <- regexpr("\\([^\\(\\)]+\\)", x[i])
l <- attr(m, "match.length")
## split at event
u <- substr(x[i], 1, m - 1)
b <- substr(x[i], m + 1, m + l - 2)
v <- substr(x[i], m + l, nchar(x)[i])
## annotate event
list_ids <- strsplit(b, "|", fixed = TRUE)
ids <- unlist(list_ids)
ids_path <- i[togroup0(list_ids)]
ids_ann <- annotateSegments(ids, features)
ann <- unlist(ids_ann)
ann_id <- togroup0(ids_ann)
ann_path <- ids_path[ann_id]
path_ann <- vector("list", length(i))
if (!is.null(ann)) {
tmp <- tapply(ann, ann_path, unique, simplify = FALSE)
path_ann[match(names(tmp), i)] <- tmp
}
path_ann <- paste0("{", unstrsplit(path_ann, ";"), "}")
x[i] <- paste0(u, path_ann, v)
i <- grep("(", x, fixed = TRUE)
}
out <- annotateSegments(x, features)
out <- as(out, "CharacterList")
## decode txName
out <- relist(txName_unique[as.integer(unlist(out))], out)
txName(paths) <- out
## geneName
path_ids <- extractIDs(featureID(paths))
path_ids_unlisted <- unlist(path_ids)
i <- match(path_ids_unlisted, featureID(features))
f <- factor(togroup0(path_ids), levels = seq_along(path_ids))
path_ann <- splitCharacterList(geneName(features)[i], f)
geneName(paths) <- setNames(path_ann, NULL)
return(paths)
}
matchTxFeatures <- function(query, subject)
{
q <- feature2name(query, TRUE)
s <- feature2name(subject, TRUE)
s2i <- split(seq_along(s), s)
qH <- which(q %in% names(s2i))
sH <- match(q[qH], names(s2i))
qH <- qH[togroup0(sH)]
sH <- unlist(sH)
Hits(qH, sH, length(query), length(subject),
sort.by.query = TRUE)
}
matchSGFeatures <- function(query, subject) {
Reduce(union, list(
matchJunction(query, subject),
matchExon(query, subject),
matchSplice(query, subject, "D"),
matchSplice(query, subject, "A")
))
}
matchJunction <- function(query, subject) {
i_q <- which(type(query) == "J")
i_s <- which(type(subject) == "J")
hits <- findMatches(query[i_q], subject[i_s])
qH <- queryHits(hits)
sH <- subjectHits(hits)
Hits(i_q[qH], i_s[sH], length(query), length(subject),
sort.by.query = TRUE)
}
matchExon <- function(query, subject, stringent = TRUE) {
i_q <- which(type(query) == "E")
i_s <- which(type(subject) %in% c("I", "F", "L", "U"))
q2 <- query[i_q]
s2 <- subject[i_s]
hits <- findOverlaps(q2, s2)
qH <- queryHits(hits)
sH <- subjectHits(hits)
hits <- Hits(i_q[qH], i_s[sH], length(query), length(subject),
sort.by.query = TRUE)
if (!stringent) { return(hits) }
## exclude hits with inconsistent 5' spliced boundary
i <- which(splice5p(q2)[qH])
if (length(i) > 0) {
q2_5p <- start(flank(q2[qH][i], -1, TRUE))
s2_5p <- start(flank(s2[sH][i], -1, TRUE))
s2_type <- type(s2)[sH][i]
excl_q_5p <- i[which(q2_5p != s2_5p | s2_type %in% c("F", "U"))]
} else { excl_q_5p <- integer() }
## exclude hits with inconsistent 3' spliced boundary
i <- which(splice3p(q2)[qH])
if (length(i) > 0) {
q2_3p <- start(flank(q2[qH][i], -1, FALSE))
s2_3p <- start(flank(s2[sH][i], -1, FALSE))
s2_type <- type(s2)[sH][i]
excl_q_3p <- i[which(q2_3p != s2_3p | s2_type %in% c("L", "U"))]
} else { excl_q_3p <- integer() }
## exclude hits with query overlapping 5' flanking intron
i <- which(type(s2)[sH] %in% c("I", "L"))
if (length(i) > 0) {
hits_2 <- findOverlaps(q2[qH][i], flank(s2[sH][i], 1, TRUE))
hits_2 <- hits_2[queryHits(hits_2) == subjectHits(hits_2)]
excl_s_5p <- i[queryHits(hits_2)]
} else { excl_s_5p <- integer() }
## exclude hits with query overlapping 3' flanking intron
i <- which(type(s2)[sH] %in% c("F", "I"))
if (length(i) > 0) {
hits_2 <- findOverlaps(q2[qH][i], flank(s2[sH][i], 1, FALSE))
hits_2 <- hits_2[queryHits(hits_2) == subjectHits(hits_2)]
excl_s_3p <- i[queryHits(hits_2)]
} else { excl_s_3p <- integer() }
excl <- unique(c(excl_q_5p, excl_q_3p, excl_s_5p, excl_s_3p))
if (length(excl) > 0) { hits <- hits[-excl] }
return(hits)
}
matchSplice <- function(query, subject, type = c("D", "A")) {
type <- match.arg(type)
i_q <- which(type(query) == type)
q <- query[i_q]
if (type == "D") {
i_s_J <- which(type(subject) == "J")
s_J <- flank(subject[i_s_J], -1, TRUE)
i_s_E <- which(type(subject) %in% c("I", "F"))
s_E <- flank(subject[i_s_E], -1, FALSE)
} else if (type == "A") {
i_s_J <- which(type(subject) == "J")
s_J <- flank(subject[i_s_J], -1, FALSE)
i_s_E <- which(type(subject) %in% c("I", "L"))
s_E <- flank(subject[i_s_E], -1, TRUE)
}
i_s <- c(i_s_J, i_s_E)
s <- c(s_J, s_E)
hits <- findMatches(q, s)
qH <- queryHits(hits)
sH <- subjectHits(hits)
Hits(i_q[qH], i_s[sH], length(query), length(subject),
sort.by.query = TRUE)
}
Try the SGSeq package in your browser
Any scripts or data that you put into this service are public.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.