R/convert.R
In ldg21/SGSeq: Splice event prediction and quantification from RNA-seq data
Defines functions
convertToSGSegments
addGeneID
addFeatureID
processFeatures
convertToSGFeatures
collapseFeatures
extractJunctions
exonFrame
extractExons
exonsOnSameChromAndStrand
convertToTxFeatures
Documented in
convertToSGFeatures
convertToTxFeatures
##' Convert a \code{TxDb} object or a \code{GRangesList} of exons
##' grouped by transcripts to a \code{TxFeatures} object.
##'
##' If \code{x} is a \code{GRangesList}, transcript names and gene names
##' can be specified as character vectors in metadata
##' columns \code{txName} and \code{geneName}, respectively.
##' If missing, transcript names are based on \code{names(x)}.
##' For import from GFF format, use function \code{importTranscripts}.
##'
##' In the returned \code{TxFeatures} object, column \code{type} takes
##' values \dQuote{J} (splice junction), \dQuote{I} (internal exon),
##' \dQuote{F} (5'/first exon), \dQuote{L} (3'/last exon) or \dQuote{U}
##' (unspliced).
##'
##' @title Convert to TxFeatures object
##' @param x \code{TxDb} object or \code{GRangesList} of exons grouped
##' by transcript. For import from GFF format, use function
##' \code{importTranscripts}.
##' @return \code{TxFeatures} object
##' @examples
##' gr <- GRanges(c(1, 1), IRanges(c(1, 201), c(100, 300)), c("+", "+"))
##' grl <- split(gr, 1)
##' txf <- convertToTxFeatures(grl)
##' @author Leonard Goldstein
convertToTxFeatures <- function(x)
{
if (is(x, "TxDb")) {
tx <- convertToTranscripts(x)
} else if (is(x, "GRangesList")) {
if (!exonsOnSameChromAndStrand(x)) {
stop("All ranges in the same element of x must be on the same
chromosome and strand")
}
if (!is.null(mcols(x)$txName)) {
names(x) <- mcols(x)$txName
} else if (is.null(names(x))) {
names(x) <- seq_along(x)
}
mcols(x)$txName <- names(x)
tx <- x
} else {
stop("x must be a TxDb or GRangesList object")
}
## reduce ranges to ensure there are no adjacent exons
tx_unlisted <- unlist(tx)
mcols(tx_unlisted) <- NULL
tx <- relist(tx_unlisted, tx)
tx_reduced <- reduce(tx)
if (sum(sum(width(tx))) != sum(sum(width(tx_reduced)))) {
stop("x includes transcripts with overlapping exons")
}
tx <- tx_reduced
## remove tx with duplicate names
dup <- names(tx)[duplicated(names(tx))]
if (length(dup) > 0) {
remove <- which(names(tx) %in% dup)
tx <- tx[-remove]
warning(paste("Removed", length(remove),
"transcripts with duplicate names"))
}
exons <- extractExons(tx)
junctions <- extractJunctions(tx)
features <- c(exons, junctions)
features <- collapseFeatures(features)
features <- TxFeatures(features)
if (is(x, "TxDb") || !is.null(mcols(x)$geneName)) {
tx_name <- txName(features)
tx_name_unlisted <- unlist(tx_name)
if (is(x, "TxDb")) {
gene_name_unlisted <- silent_select(x, tx_name_unlisted,
"GENEID", "TXNAME")$GENEID
} else {
gene_name_unlisted <- mcols(x)$geneName[match(tx_name_unlisted,
mcols(x)$txName)]
}
i_not_na <- which(!is.na(gene_name_unlisted))
i_gene_name <- split(gene_name_unlisted[i_not_na],
togroup0(tx_name)[i_not_na])
i_gene_name <- CharacterList(i_gene_name)
i_gene_name <- unique(i_gene_name)
gene_name <- CharacterList(vector("list", length(features)))
gene_name[as.integer(names(i_gene_name))] <- i_gene_name
geneName(features) <- gene_name
}
return(features)
}
exonsOnSameChromAndStrand <- function(x)
{
sn <- unique(CharacterList(seqnames(x)))
st <- unique(CharacterList(strand(x)))
if (any(elementNROWS(sn) > 1) || any(elementNROWS(st) > 1)) {
valid <- FALSE
} else {
valid <- TRUE
}
return(valid)
}
extractExons <- function(tx)
{
tx <- reorderFeatures(tx)
exons <- setNames(unlist(tx), NULL)
exons_tx <- togroup0(tx)
tx_i_exon <- IntegerList(split(seq_along(exons), exons_tx))
i_X <- pfirst(tx_i_exon)
i_Y <- plast(tx_i_exon)
type <- rep("I", length(exons))
type[i_X] <- "F"
type[i_Y] <- "L"
type[intersect(i_X, i_Y)] <- "U"
mcols(exons) <- DataFrame(
type = type,
txName = as(names(tx)[exons_tx], "CharacterList"))
if (!is.null(mcols(tx)$cdsStart) && !is.null(mcols(tx)$cdsEnd) &&
!is.null(mcols(tx)$status)) {
exons <- exonFrame(exons, exons_tx, tx)
}
return(exons)
}
exonFrame <- function(ex, ex_tx, tx)
{
tx_chrom <- as.character(seqnames(unlist(range(tx))))
tx_strand <- as.character(strand(unlist(range(tx))))
tx_cdsStart <- mcols(tx)$cdsStart
tx_cdsEnd <- mcols(tx)$cdsEnd
tx_status <- mcols(tx)$status
i_tx_coding <- which(!is.na(tx_cdsStart) & !is.na(tx_cdsEnd))
tx_coding_cds <- GRanges(
tx_chrom[i_tx_coding],
IRanges(tx_cdsStart[i_tx_coding], tx_cdsEnd[i_tx_coding]),
tx_strand[i_tx_coding]
)
hits <- findOverlaps(ex, tx_coding_cds)
hits <- hits[ex_tx[queryHits(hits)] == i_tx_coding[subjectHits(hits)]]
i_ex_coding <- queryHits(hits)
ex_coding <- ex[i_ex_coding]
ex_coding_tx <- ex_tx[i_ex_coding]
tx_i_ex_coding <- IntegerList(split(seq_along(ex_coding), ex_coding_tx))
i_5p <- pfirst(tx_i_ex_coding, use_names = TRUE)
i_3p <- plast(tx_i_ex_coding, use_names = TRUE)
i_5p_pos <- i_5p[which(strand(ex_coding)[i_5p] == "+")]
i_5p_neg <- i_5p[which(strand(ex_coding)[i_5p] == "-")]
i_3p_pos <- i_3p[which(strand(ex_coding)[i_3p] == "+")]
i_3p_neg <- i_3p[which(strand(ex_coding)[i_3p] == "-")]
## set frame for coding exons
ex_coding_cds <- restrict(ex_coding, start = tx_cdsStart[ex_coding_tx],
end = tx_cdsEnd[ex_coding_tx])
ex_coding_cds_length <- unlist(tapply(width(ex_coding_cds),
ex_coding_tx, cumsum), use.names = FALSE)
ex_coding_cds_offset <- c(NA_integer_,
ex_coding_cds_length[-length(ex_coding_cds_length)])
ex_coding_cds_offset[i_5p_pos] <- start(ex_coding)[i_5p_pos] -
start(ex_coding_cds)[i_5p_pos]
ex_coding_cds_offset[i_5p_neg] <- end(ex_coding_cds)[i_5p_neg] -
end(ex_coding)[i_5p_neg]
ex_coding_frame <- ex_coding_cds_offset %% 3
## exclude transcripts with invalid coding sequence
tx_invalid <- as.integer(names(i_3p))[which(
ex_coding_cds_length[i_3p] %% 3 != 0)]
ex_coding_frame[ex_coding_tx %in% tx_invalid] <- NA_integer_
## set frame for all exons
ex_frame <- ifelse(is.na(tx_status[ex_tx]), NA_integer_, -1)
ex_frame[i_ex_coding] <- ex_coding_frame
mcols(ex)$frame <- as.integer(ex_frame)
## set cdsStart / cdsEnd for all exons
ex_cdsStart <- rep(NA_integer_, length(ex))
ex_cdsStart[i_ex_coding][i_5p_pos] <- tx_cdsStart[ex_coding_tx][i_5p_pos] -
start(ex_coding)[i_5p_pos]
ex_cdsStart[i_ex_coding][i_5p_neg] <- end(ex_coding)[i_5p_neg] -
tx_cdsEnd[ex_coding_tx][i_5p_neg]
ex_cdsStart[ex_tx %in% tx_invalid] <- NA_integer_
mcols(ex)$cdsStart <- as.integer(ex_cdsStart)
ex_cdsEnd <- rep(NA_integer_, length(ex))
ex_cdsEnd[i_ex_coding][i_3p_pos] <- tx_cdsEnd[ex_coding_tx][i_3p_pos] -
start(ex_coding)[i_3p_pos] + 1
ex_cdsEnd[i_ex_coding][i_3p_neg] <- end(ex_coding)[i_3p_neg] -
tx_cdsStart[ex_coding_tx][i_3p_neg] + 1
ex_cdsEnd[ex_tx %in% tx_invalid] <- NA_integer_
mcols(ex)$cdsEnd <- as.integer(ex_cdsEnd)
return(ex)
}
extractJunctions <- function(tx)
{
introns <- setdiff(range(tx), tx)
junctions <- setNames(unlist(introns), NULL) + 1
mcols(junctions) <- DataFrame(
type = rep("J", length(junctions)),
txName = as(names(introns)[togroup0(introns)], "CharacterList"))
if (!is.null(mcols(tx)$cdsStart) && !is.null(mcols(tx)$cdsEnd) &&
!is.null(mcols(tx)$status)) {
for (k in c("frame", "cdsStart", "cdsEnd")) {
mcols(junctions)[[k]] <- rep(NA_integer_, length(junctions))
}
}
return(junctions)
}
collapseFeatures <- function(features)
{
features_name <- factor(feature2name(features))
collapsed <- features[match(levels(features_name), features_name)]
mcols(collapsed)$txName <- setNames(splitCharacterList(
mcols(features)$txName, features_name), NULL)
if (!is.null(mcols(features)$frame)) {
cols <- c("frame", "cdsStart", "cdsEnd")
x <- paste(
mcols(features)$frame,
mcols(features)$cdsStart,
mcols(features)$cdsEnd,
sep = ",")
x <- tapply(x, features_name, setdiff, "NA,NA,NA", simplify = FALSE)
y <- strsplit(unlist(x), ",")
for (j in seq_along(cols)) {
z <- relist(suppressWarnings(
as.integer(vapply(y, "[", character(1), j))), x)
z <- IntegerList(z)
mcols(collapsed)[[cols[j]]] <- setNames(z, NULL)
}
}
collapsed <- sort(collapsed)
return(collapsed)
}
##' Convert transcript features (predicted from RNA-seq data or
##' extracted from transcript annotation) to splice graph features.
##'
##' Splice junctions are unaltered. Exons are disjoined into
##' non-overlapping exon bins. Adjacent exon bins without a splice site
##' at the shared boundary are merged.
##'
##' Entries for splice donor and acceptor sites (positions immediately
##' upstream and downstream of introns, respectively) are added.
##'
##' In the returned \code{SGFeatures} object, column \code{type} takes
##' values \dQuote{J} (splice junction), \dQuote{E} (exon bin),
##' \dQuote{D} (splice donor) or \dQuote{A} (splice acceptor).
##' Columns \code{splice5p} and \code{splice3p} indicate mandatory
##' splices at the 5' and 3' end of exon bins, respectively
##' (determining whether reads overlapping exon boundaries must be
##' spliced at the boundary to be considered compatible).
##' \code{splice5p} (\code{splice3p}) is \code{TRUE} if the first (last)
##' position of the exon coincides with a splice acceptor (donor)
##' and it is not adjacent to a neighboring exon bin.
##'
##' Each feature is assigned a unique feature and gene identifier,
##' stored in columns \code{featureID} and \code{geneID},
##' respectively. The latter indicates features that belong to the
##' same gene, represented by a connected component in the splice graph.
##'
##' @title Convert transcript features to splice graph features
##' @param x \code{TxFeatures} object
##' @param coerce Logical indicating whether transcript features
##' should be coerced to splice graph features without disjoining
##' exons and omitting splice donor and acceptor sites
##' @return \code{SGFeatures} object
##' @examples
##' sgf <- convertToSGFeatures(txf_ann)
##' @author Leonard Goldstein
convertToSGFeatures <- function(x, coerce = FALSE)
{
if (!is(x, "TxFeatures")) {
stop("x must be a TxFeatures object")
}
if (length(x) == 0) {
return(SGFeatures())
}
if (coerce) {
features <- granges(x)
mcols(features)$type <- as.character(type(x))
splice5p <- mcols(features)$type %in% c("I", "L")
splice3p <- mcols(features)$type %in% c("I", "F")
splice5p[mcols(features)$type == "J"] <- NA
splice3p[mcols(features)$type == "J"] <- NA
mcols(features)$type[mcols(features)$type != "J"] <- "E"
mcols(features)$splice5p <- splice5p
mcols(features)$splice3p <- splice3p
mcols(features)$txName <- txName(x)
mcols(features)$geneName <- geneName(x)
} else {
features <- processFeatures(x)
}
features <- addFeatureID(features)
features <- addGeneID(features)
features <- SGFeatures(features)
if (!coerce) {
features <- annotate(features, x)
}
return(features)
}
processFeatures <- function(features)
{
junctions <- granges(features)[type(features) == "J"]
junctions_D <- flank(junctions, -1, TRUE)
junctions_A <- flank(junctions, -1, FALSE)
mcols(junctions)$type <- rep("J", length(junctions))
if (is(features, "TxFeatures")) {
exons <- features[type(features) %in% c("I", "F", "L", "U")]
exons_D <- flank(features[type(features) %in% c("I", "F")], -1, FALSE)
exons_A <- flank(features[type(features) %in% c("I", "L")], -1, TRUE)
} else if (is(features, "SGFeatures")) {
exons <- features[type(features) == "E"]
exons_D <- flank(features[splice3p(features)], -1, FALSE)
exons_A <- flank(features[splice5p(features)], -1, TRUE)
}
exons <- granges(exons)
exons_D <- granges(exons_D)
exons_A <- granges(exons_A)
D <- unique(c(junctions_D, exons_D))
mcols(D)$type <- rep("D", length(D))
A <- unique(c(junctions_A, exons_A))
mcols(A)$type <- rep("A", length(A))
splicesites <- c(D, A)
other <- c(junctions, splicesites)
## Disjoin exons into non-overlapping exon bins,
## merge adjacent exon bins that do not have a
## splice site at the shared boundary
exons <- disjoin(exons)
exons_start <- flank(exons, -1, TRUE)
exons_end <- flank(exons, -1, FALSE)
i_q <- which(!exons_end %over% splicesites)
i_s <- which(!exons_start %over% splicesites)
ol <- findOverlaps(suppressWarnings(flank(exons[i_q], 1, FALSE)),
exons_start[i_s])
if (length(ol) > 0) {
qH <- i_q[queryHits(ol)]
sH <- i_s[subjectHits(ol)]
i_to_be_merged <- union(qH, sH)
d <- data.frame(from = qH, to = sH)
v <- data.frame(name = i_to_be_merged)
g <- graph.data.frame(d = d, directed = TRUE, vertices = v)
k <- clusters(g)$membership
exons_to_be_merged <- split(exons[i_to_be_merged], k)
exons_merged <- unlist(reduce(exons_to_be_merged))
if (length(exons_to_be_merged) != length(exons_merged)) {
stop("cannot merge non-adjacent exons")
}
exons <- c(exons[-i_to_be_merged], exons_merged)
}
exons_start <- flank(exons, -1, TRUE)
exons_end <- flank(exons, -1, FALSE)
splice5p <- rep(FALSE, length(exons))
i_spliced <- unique(queryHits(findOverlaps(exons_start, A)))
i_adjacent <- unique(queryHits(findOverlaps(
suppressWarnings(flank(exons, 1, TRUE)), exons)))
splice5p[setdiff(i_spliced, i_adjacent)] <- TRUE
splice3p <- rep(FALSE, length(exons))
i_spliced <- unique(queryHits(findOverlaps(exons_end, D)))
i_adjacent <- unique(queryHits(findOverlaps(
suppressWarnings(flank(exons, 1, FALSE)), exons)))
splice3p[setdiff(i_spliced, i_adjacent)] <- TRUE
mcols(exons)$type <- rep("E", length(exons))
mcols(exons)$splice5p <- splice5p
mcols(exons)$splice3p <- splice3p
mcols(other)$splice5p <- rep(NA, length(other))
mcols(other)$splice3p <- rep(NA, length(other))
## combine exons and other features
features <- setNames(c(exons, other), NULL)
features <- sort(features)
return(features)
}
addFeatureID <- function(features)
{
mcols(features)$featureID <- seq_along(features)
return(features)
}
addGeneID <- function(features)
{
g <- spliceGraph(features)
gd <- edges(g)
gv <- nodes(g)
geneID <- rep(NA, length(features))
geneID[as.integer(gd$featureID)] <- gd$geneID
i <- which(!is.na(gv$featureID))
geneID[as.integer(gv$featureID)[i]] <- gv$geneID[i]
mcols(features)$geneID <- geneID
return(features)
}
convertToSGSegments <- function(x, cores = 1)
{
x_segmentID <- findSGSegments(x, cores)
i <- which(!is.na(x_segmentID))
segments <- split(x[i], x_segmentID[i])
segments <- reorderFeatures(segments)
list_type <- split(as.character(type(unlist(segments))),
togroup0(segments))
list_featureID <- CharacterList(split(featureID(unlist(segments)),
togroup0(segments)))
gd <- edges(spliceGraph(x))
i_first <- match(pfirst(list_featureID), gd$featureID)
i_last <- match(plast(list_featureID), gd$featureID)
mcols(segments) <- DataFrame(
from = gd$from[i_first],
to = gd$to[i_last],
type = unstrsplit(list_type, ""),
splice5p = gd$splice5p[i_first],
splice3p = gd$splice3p[i_last],
featureID = unstrsplit(list_featureID, ","),
segmentID = seq_along(segments),
geneID = gd$geneID[i_first])
segments <- SGSegments(segments)
segments <- annotatePaths(segments)
return(segments)
}
ldg21/SGSeq documentation built on Oct. 14, 2020, 9:51 p.m.
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Defines functions convertToSGSegments addGeneID addFeatureID processFeatures convertToSGFeatures collapseFeatures extractJunctions exonFrame extractExons exonsOnSameChromAndStrand convertToTxFeatures
Documented in convertToSGFeatures convertToTxFeatures
##' Convert a \code{TxDb} object or a \code{GRangesList} of exons
##' grouped by transcripts to a \code{TxFeatures} object.
##'
##' If \code{x} is a \code{GRangesList}, transcript names and gene names
##' can be specified as character vectors in metadata
##' columns \code{txName} and \code{geneName}, respectively.
##' If missing, transcript names are based on \code{names(x)}.
##' For import from GFF format, use function \code{importTranscripts}.
##'
##' In the returned \code{TxFeatures} object, column \code{type} takes
##' values \dQuote{J} (splice junction), \dQuote{I} (internal exon),
##' \dQuote{F} (5'/first exon), \dQuote{L} (3'/last exon) or \dQuote{U}
##' (unspliced).
##'
##' @title Convert to TxFeatures object
##' @param x \code{TxDb} object or \code{GRangesList} of exons grouped
##' by transcript. For import from GFF format, use function
##' \code{importTranscripts}.
##' @return \code{TxFeatures} object
##' @examples
##' gr <- GRanges(c(1, 1), IRanges(c(1, 201), c(100, 300)), c("+", "+"))
##' grl <- split(gr, 1)
##' txf <- convertToTxFeatures(grl)
##' @author Leonard Goldstein
convertToTxFeatures <- function(x)
{
if (is(x, "TxDb")) {
tx <- convertToTranscripts(x)
} else if (is(x, "GRangesList")) {
if (!exonsOnSameChromAndStrand(x)) {
stop("All ranges in the same element of x must be on the same
chromosome and strand")
}
if (!is.null(mcols(x)$txName)) {
names(x) <- mcols(x)$txName
} else if (is.null(names(x))) {
names(x) <- seq_along(x)
}
mcols(x)$txName <- names(x)
tx <- x
} else {
stop("x must be a TxDb or GRangesList object")
}
## reduce ranges to ensure there are no adjacent exons
tx_unlisted <- unlist(tx)
mcols(tx_unlisted) <- NULL
tx <- relist(tx_unlisted, tx)
tx_reduced <- reduce(tx)
if (sum(sum(width(tx))) != sum(sum(width(tx_reduced)))) {
stop("x includes transcripts with overlapping exons")
}
tx <- tx_reduced
## remove tx with duplicate names
dup <- names(tx)[duplicated(names(tx))]
if (length(dup) > 0) {
remove <- which(names(tx) %in% dup)
tx <- tx[-remove]
warning(paste("Removed", length(remove),
"transcripts with duplicate names"))
}
exons <- extractExons(tx)
junctions <- extractJunctions(tx)
features <- c(exons, junctions)
features <- collapseFeatures(features)
features <- TxFeatures(features)
if (is(x, "TxDb") || !is.null(mcols(x)$geneName)) {
tx_name <- txName(features)
tx_name_unlisted <- unlist(tx_name)
if (is(x, "TxDb")) {
gene_name_unlisted <- silent_select(x, tx_name_unlisted,
"GENEID", "TXNAME")$GENEID
} else {
gene_name_unlisted <- mcols(x)$geneName[match(tx_name_unlisted,
mcols(x)$txName)]
}
i_not_na <- which(!is.na(gene_name_unlisted))
i_gene_name <- split(gene_name_unlisted[i_not_na],
togroup0(tx_name)[i_not_na])
i_gene_name <- CharacterList(i_gene_name)
i_gene_name <- unique(i_gene_name)
gene_name <- CharacterList(vector("list", length(features)))
gene_name[as.integer(names(i_gene_name))] <- i_gene_name
geneName(features) <- gene_name
}
return(features)
}
exonsOnSameChromAndStrand <- function(x)
{
sn <- unique(CharacterList(seqnames(x)))
st <- unique(CharacterList(strand(x)))
if (any(elementNROWS(sn) > 1) || any(elementNROWS(st) > 1)) {
valid <- FALSE
} else {
valid <- TRUE
}
return(valid)
}
extractExons <- function(tx)
{
tx <- reorderFeatures(tx)
exons <- setNames(unlist(tx), NULL)
exons_tx <- togroup0(tx)
tx_i_exon <- IntegerList(split(seq_along(exons), exons_tx))
i_X <- pfirst(tx_i_exon)
i_Y <- plast(tx_i_exon)
type <- rep("I", length(exons))
type[i_X] <- "F"
type[i_Y] <- "L"
type[intersect(i_X, i_Y)] <- "U"
mcols(exons) <- DataFrame(
type = type,
txName = as(names(tx)[exons_tx], "CharacterList"))
if (!is.null(mcols(tx)$cdsStart) && !is.null(mcols(tx)$cdsEnd) &&
!is.null(mcols(tx)$status)) {
exons <- exonFrame(exons, exons_tx, tx)
}
return(exons)
}
exonFrame <- function(ex, ex_tx, tx)
{
tx_chrom <- as.character(seqnames(unlist(range(tx))))
tx_strand <- as.character(strand(unlist(range(tx))))
tx_cdsStart <- mcols(tx)$cdsStart
tx_cdsEnd <- mcols(tx)$cdsEnd
tx_status <- mcols(tx)$status
i_tx_coding <- which(!is.na(tx_cdsStart) & !is.na(tx_cdsEnd))
tx_coding_cds <- GRanges(
tx_chrom[i_tx_coding],
IRanges(tx_cdsStart[i_tx_coding], tx_cdsEnd[i_tx_coding]),
tx_strand[i_tx_coding]
)
hits <- findOverlaps(ex, tx_coding_cds)
hits <- hits[ex_tx[queryHits(hits)] == i_tx_coding[subjectHits(hits)]]
i_ex_coding <- queryHits(hits)
ex_coding <- ex[i_ex_coding]
ex_coding_tx <- ex_tx[i_ex_coding]
tx_i_ex_coding <- IntegerList(split(seq_along(ex_coding), ex_coding_tx))
i_5p <- pfirst(tx_i_ex_coding, use_names = TRUE)
i_3p <- plast(tx_i_ex_coding, use_names = TRUE)
i_5p_pos <- i_5p[which(strand(ex_coding)[i_5p] == "+")]
i_5p_neg <- i_5p[which(strand(ex_coding)[i_5p] == "-")]
i_3p_pos <- i_3p[which(strand(ex_coding)[i_3p] == "+")]
i_3p_neg <- i_3p[which(strand(ex_coding)[i_3p] == "-")]
## set frame for coding exons
ex_coding_cds <- restrict(ex_coding, start = tx_cdsStart[ex_coding_tx],
end = tx_cdsEnd[ex_coding_tx])
ex_coding_cds_length <- unlist(tapply(width(ex_coding_cds),
ex_coding_tx, cumsum), use.names = FALSE)
ex_coding_cds_offset <- c(NA_integer_,
ex_coding_cds_length[-length(ex_coding_cds_length)])
ex_coding_cds_offset[i_5p_pos] <- start(ex_coding)[i_5p_pos] -
start(ex_coding_cds)[i_5p_pos]
ex_coding_cds_offset[i_5p_neg] <- end(ex_coding_cds)[i_5p_neg] -
end(ex_coding)[i_5p_neg]
ex_coding_frame <- ex_coding_cds_offset %% 3
## exclude transcripts with invalid coding sequence
tx_invalid <- as.integer(names(i_3p))[which(
ex_coding_cds_length[i_3p] %% 3 != 0)]
ex_coding_frame[ex_coding_tx %in% tx_invalid] <- NA_integer_
## set frame for all exons
ex_frame <- ifelse(is.na(tx_status[ex_tx]), NA_integer_, -1)
ex_frame[i_ex_coding] <- ex_coding_frame
mcols(ex)$frame <- as.integer(ex_frame)
## set cdsStart / cdsEnd for all exons
ex_cdsStart <- rep(NA_integer_, length(ex))
ex_cdsStart[i_ex_coding][i_5p_pos] <- tx_cdsStart[ex_coding_tx][i_5p_pos] -
start(ex_coding)[i_5p_pos]
ex_cdsStart[i_ex_coding][i_5p_neg] <- end(ex_coding)[i_5p_neg] -
tx_cdsEnd[ex_coding_tx][i_5p_neg]
ex_cdsStart[ex_tx %in% tx_invalid] <- NA_integer_
mcols(ex)$cdsStart <- as.integer(ex_cdsStart)
ex_cdsEnd <- rep(NA_integer_, length(ex))
ex_cdsEnd[i_ex_coding][i_3p_pos] <- tx_cdsEnd[ex_coding_tx][i_3p_pos] -
start(ex_coding)[i_3p_pos] + 1
ex_cdsEnd[i_ex_coding][i_3p_neg] <- end(ex_coding)[i_3p_neg] -
tx_cdsStart[ex_coding_tx][i_3p_neg] + 1
ex_cdsEnd[ex_tx %in% tx_invalid] <- NA_integer_
mcols(ex)$cdsEnd <- as.integer(ex_cdsEnd)
return(ex)
}
extractJunctions <- function(tx)
{
introns <- setdiff(range(tx), tx)
junctions <- setNames(unlist(introns), NULL) + 1
mcols(junctions) <- DataFrame(
type = rep("J", length(junctions)),
txName = as(names(introns)[togroup0(introns)], "CharacterList"))
if (!is.null(mcols(tx)$cdsStart) && !is.null(mcols(tx)$cdsEnd) &&
!is.null(mcols(tx)$status)) {
for (k in c("frame", "cdsStart", "cdsEnd")) {
mcols(junctions)[[k]] <- rep(NA_integer_, length(junctions))
}
}
return(junctions)
}
collapseFeatures <- function(features)
{
features_name <- factor(feature2name(features))
collapsed <- features[match(levels(features_name), features_name)]
mcols(collapsed)$txName <- setNames(splitCharacterList(
mcols(features)$txName, features_name), NULL)
if (!is.null(mcols(features)$frame)) {
cols <- c("frame", "cdsStart", "cdsEnd")
x <- paste(
mcols(features)$frame,
mcols(features)$cdsStart,
mcols(features)$cdsEnd,
sep = ",")
x <- tapply(x, features_name, setdiff, "NA,NA,NA", simplify = FALSE)
y <- strsplit(unlist(x), ",")
for (j in seq_along(cols)) {
z <- relist(suppressWarnings(
as.integer(vapply(y, "[", character(1), j))), x)
z <- IntegerList(z)
mcols(collapsed)[[cols[j]]] <- setNames(z, NULL)
}
}
collapsed <- sort(collapsed)
return(collapsed)
}
##' Convert transcript features (predicted from RNA-seq data or
##' extracted from transcript annotation) to splice graph features.
##'
##' Splice junctions are unaltered. Exons are disjoined into
##' non-overlapping exon bins. Adjacent exon bins without a splice site
##' at the shared boundary are merged.
##'
##' Entries for splice donor and acceptor sites (positions immediately
##' upstream and downstream of introns, respectively) are added.
##'
##' In the returned \code{SGFeatures} object, column \code{type} takes
##' values \dQuote{J} (splice junction), \dQuote{E} (exon bin),
##' \dQuote{D} (splice donor) or \dQuote{A} (splice acceptor).
##' Columns \code{splice5p} and \code{splice3p} indicate mandatory
##' splices at the 5' and 3' end of exon bins, respectively
##' (determining whether reads overlapping exon boundaries must be
##' spliced at the boundary to be considered compatible).
##' \code{splice5p} (\code{splice3p}) is \code{TRUE} if the first (last)
##' position of the exon coincides with a splice acceptor (donor)
##' and it is not adjacent to a neighboring exon bin.
##'
##' Each feature is assigned a unique feature and gene identifier,
##' stored in columns \code{featureID} and \code{geneID},
##' respectively. The latter indicates features that belong to the
##' same gene, represented by a connected component in the splice graph.
##'
##' @title Convert transcript features to splice graph features
##' @param x \code{TxFeatures} object
##' @param coerce Logical indicating whether transcript features
##' should be coerced to splice graph features without disjoining
##' exons and omitting splice donor and acceptor sites
##' @return \code{SGFeatures} object
##' @examples
##' sgf <- convertToSGFeatures(txf_ann)
##' @author Leonard Goldstein
convertToSGFeatures <- function(x, coerce = FALSE)
{
if (!is(x, "TxFeatures")) {
stop("x must be a TxFeatures object")
}
if (length(x) == 0) {
return(SGFeatures())
}
if (coerce) {
features <- granges(x)
mcols(features)$type <- as.character(type(x))
splice5p <- mcols(features)$type %in% c("I", "L")
splice3p <- mcols(features)$type %in% c("I", "F")
splice5p[mcols(features)$type == "J"] <- NA
splice3p[mcols(features)$type == "J"] <- NA
mcols(features)$type[mcols(features)$type != "J"] <- "E"
mcols(features)$splice5p <- splice5p
mcols(features)$splice3p <- splice3p
mcols(features)$txName <- txName(x)
mcols(features)$geneName <- geneName(x)
} else {
features <- processFeatures(x)
}
features <- addFeatureID(features)
features <- addGeneID(features)
features <- SGFeatures(features)
if (!coerce) {
features <- annotate(features, x)
}
return(features)
}
processFeatures <- function(features)
{
junctions <- granges(features)[type(features) == "J"]
junctions_D <- flank(junctions, -1, TRUE)
junctions_A <- flank(junctions, -1, FALSE)
mcols(junctions)$type <- rep("J", length(junctions))
if (is(features, "TxFeatures")) {
exons <- features[type(features) %in% c("I", "F", "L", "U")]
exons_D <- flank(features[type(features) %in% c("I", "F")], -1, FALSE)
exons_A <- flank(features[type(features) %in% c("I", "L")], -1, TRUE)
} else if (is(features, "SGFeatures")) {
exons <- features[type(features) == "E"]
exons_D <- flank(features[splice3p(features)], -1, FALSE)
exons_A <- flank(features[splice5p(features)], -1, TRUE)
}
exons <- granges(exons)
exons_D <- granges(exons_D)
exons_A <- granges(exons_A)
D <- unique(c(junctions_D, exons_D))
mcols(D)$type <- rep("D", length(D))
A <- unique(c(junctions_A, exons_A))
mcols(A)$type <- rep("A", length(A))
splicesites <- c(D, A)
other <- c(junctions, splicesites)
## Disjoin exons into non-overlapping exon bins,
## merge adjacent exon bins that do not have a
## splice site at the shared boundary
exons <- disjoin(exons)
exons_start <- flank(exons, -1, TRUE)
exons_end <- flank(exons, -1, FALSE)
i_q <- which(!exons_end %over% splicesites)
i_s <- which(!exons_start %over% splicesites)
ol <- findOverlaps(suppressWarnings(flank(exons[i_q], 1, FALSE)),
exons_start[i_s])
if (length(ol) > 0) {
qH <- i_q[queryHits(ol)]
sH <- i_s[subjectHits(ol)]
i_to_be_merged <- union(qH, sH)
d <- data.frame(from = qH, to = sH)
v <- data.frame(name = i_to_be_merged)
g <- graph.data.frame(d = d, directed = TRUE, vertices = v)
k <- clusters(g)$membership
exons_to_be_merged <- split(exons[i_to_be_merged], k)
exons_merged <- unlist(reduce(exons_to_be_merged))
if (length(exons_to_be_merged) != length(exons_merged)) {
stop("cannot merge non-adjacent exons")
}
exons <- c(exons[-i_to_be_merged], exons_merged)
}
exons_start <- flank(exons, -1, TRUE)
exons_end <- flank(exons, -1, FALSE)
splice5p <- rep(FALSE, length(exons))
i_spliced <- unique(queryHits(findOverlaps(exons_start, A)))
i_adjacent <- unique(queryHits(findOverlaps(
suppressWarnings(flank(exons, 1, TRUE)), exons)))
splice5p[setdiff(i_spliced, i_adjacent)] <- TRUE
splice3p <- rep(FALSE, length(exons))
i_spliced <- unique(queryHits(findOverlaps(exons_end, D)))
i_adjacent <- unique(queryHits(findOverlaps(
suppressWarnings(flank(exons, 1, FALSE)), exons)))
splice3p[setdiff(i_spliced, i_adjacent)] <- TRUE
mcols(exons)$type <- rep("E", length(exons))
mcols(exons)$splice5p <- splice5p
mcols(exons)$splice3p <- splice3p
mcols(other)$splice5p <- rep(NA, length(other))
mcols(other)$splice3p <- rep(NA, length(other))
## combine exons and other features
features <- setNames(c(exons, other), NULL)
features <- sort(features)
return(features)
}
addFeatureID <- function(features)
{
mcols(features)$featureID <- seq_along(features)
return(features)
}
addGeneID <- function(features)
{
g <- spliceGraph(features)
gd <- edges(g)
gv <- nodes(g)
geneID <- rep(NA, length(features))
geneID[as.integer(gd$featureID)] <- gd$geneID
i <- which(!is.na(gv$featureID))
geneID[as.integer(gv$featureID)[i]] <- gv$geneID[i]
mcols(features)$geneID <- geneID
return(features)
}
convertToSGSegments <- function(x, cores = 1)
{
x_segmentID <- findSGSegments(x, cores)
i <- which(!is.na(x_segmentID))
segments <- split(x[i], x_segmentID[i])
segments <- reorderFeatures(segments)
list_type <- split(as.character(type(unlist(segments))),
togroup0(segments))
list_featureID <- CharacterList(split(featureID(unlist(segments)),
togroup0(segments)))
gd <- edges(spliceGraph(x))
i_first <- match(pfirst(list_featureID), gd$featureID)
i_last <- match(plast(list_featureID), gd$featureID)
mcols(segments) <- DataFrame(
from = gd$from[i_first],
to = gd$to[i_last],
type = unstrsplit(list_type, ""),
splice5p = gd$splice5p[i_first],
splice3p = gd$splice3p[i_last],
featureID = unstrsplit(list_featureID, ","),
segmentID = seq_along(segments),
geneID = gd$geneID[i_first])
segments <- SGSegments(segments)
segments <- annotatePaths(segments)
return(segments)
}
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