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Update prepareLinksDatabase.R #3

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152 changes: 99 additions & 53 deletions R/prepareLinksDatabase.R
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Original file line number Diff line number Diff line change
Expand Up @@ -20,107 +20,138 @@ prepareLinksDatabase <- function(annotation, tss.window, tes.window) {
txdb <- GenomicFeatures::makeTxDbFromGRanges(annotation)
ebt <- GenomicFeatures::exonsBy(txdb, by = "tx", use.names = TRUE)
t2g <- AnnotationDbi::select(txdb,
keys = names(ebt),
keytype = "TXNAME",
columns = "GENEID")
keys = names(ebt),
keytype = "TXNAME",
columns = "GENEID"
)
e2 <- BiocGenerics::unlist(ebt)
e2$transcript_id <- names(e2)
e2$gene_id = t2g$GENEID[match(e2$transcript_id, t2g$TXNAME)]
e2$gene_id <- t2g$GENEID[match(e2$transcript_id, t2g$TXNAME)]
e2$exon_id <- e2$exon_name
e2$exon_name <- NULL
e2$type <- "exon"
names(e2) <- NULL
mcols(e2) <- mcols(e2)[, c("exon_id", "exon_rank",
"transcript_id", "gene_id", "type")]
mcols(e2) <- mcols(e2)[, c(
"exon_id", "exon_rank",
"transcript_id", "gene_id", "type"
)]
bins <- list()
# TSS data base
# take first position per transcript and make it single nt
tss.bins <-
strandSort(plyranges::mutate(plyranges::anchor_5p(dplyr::filter(e2, exon_rank ==
1)), width = 1))
tss.bins <-
strandSort(
plyranges::mutate(
plyranges::anchor_5p(
dplyr::filter(e2, exon_rank == 1)), width = 1))
# make unique TSS starts merging in a 50nt window.
cat("Preparing TSSBase\n")
message("Preparing TSSBase")
tss.base <-
strandSort(
GenomicRanges::makeGRangesFromDataFrame(
reshape::melt(GenomicRanges::reduce(
GenomicRanges::split(tss.bins, ~gene_id),
min.gapwidth = tss.window)),
min.gapwidth = tss.window
)),
keep.extra.columns = TRUE
)
)
bins$tss.bins <- tss.bins
bins$tss.base <- tss.base
tss.base <-
tibble::as_tibble(tss.base) %>% dplyr::group_by(value.group_name) %>%
dplyr::mutate(count = paste0(value.group_name, ":P", sprintf("%02d", sequence(dplyr::n(
))))) %>%
tibble::as_tibble(tss.base) %>%
dplyr::group_by(value.group_name) %>%
dplyr::mutate(
count = paste0(value.group_name, ":P",
sprintf("%02d", sequence(dplyr::n())))) %>%
GenomicRanges::makeGRangesFromDataFrame(., keep.extra.columns = TRUE)
# annotate isoforms with promoter_id
ii <- GenomicRanges::findOverlaps(tss.bins, tss.base, maxgap = tss.window - 1)
tss.bins.annot <-
GenomicRanges::makeGRangesFromDataFrame(rbind(data.frame(tss.bins[S4Vectors::queryHits(ii)],
tss.base[S4Vectors::subjectHits(ii)])), keep.extra.columns = TRUE)
GenomicRanges::makeGRangesFromDataFrame(rbind(data.frame(
tss.bins[S4Vectors::queryHits(ii)],
tss.base[S4Vectors::subjectHits(ii)]
)), keep.extra.columns = TRUE)
tss.bins.annot <-
tss.bins.annot %>% dplyr::mutate(transcript_id = transcript_id, promoter_id =
count) %>%
tss.bins.annot %>%
dplyr::mutate(
transcript_id = transcript_id,
promoter_id = count
) %>%
plyranges::select(gene_id, transcript_id, promoter_id)
# TES data base
# last exon per transcript
le <-
GenomicRanges::makeGRangesFromDataFrame(
e2 %>% group_by(transcript_id) %>% dplyr::filter(exon_rank == max(exon_rank)),
e2 %>%
as.data.frame(.) %>%
group_by(transcript_id) %>%
dplyr::filter(exon_rank == max(exon_rank)),
keep.extra.columns = TRUE
)
tes.bins <-
strandSort(plyranges::mutate(plyranges::anchor_3p(le), width = 1))
# make unique TSS starts merging in a 50nt window.
cat("PrepEndBase")
tes.bins <- strandSort(
plyranges::mutate(plyranges::anchor_3p(le), width = 1))
# make unique TES starts merging in a 50nt window.
message("Preparing TES database")
tes.base <-
strandSort (
strandSort(
GenomicRanges::makeGRangesFromDataFrame(
reshape::melt(GenomicRanges::reduce((
GenomicRanges::split(tes.bins, ~ gene_id)
),
min.gapwidth =
tes.window)),
reshape::melt(GenomicRanges::reduce(
(
GenomicRanges::split(tes.bins, ~gene_id)
),
min.gapwidth =
tes.window
)),
keep.extra.columns = TRUE
)
)
tes.base <-
tibble::as.tibble(tes.base) %>% dplyr::group_by(value.group_name) %>%
dplyr::mutate(count = paste0(value.group_name, ":TE", sprintf("%02d", sequence(dplyr::n(
))))) %>%
tibble::as.tibble(tes.base) %>%
dplyr::group_by(value.group_name) %>%
dplyr::mutate(
count = paste0(value.group_name, ":TE",
sprintf("%02d", sequence(dplyr::n())))) %>%
GenomicRanges::makeGRangesFromDataFrame(., keep.extra.columns = TRUE)
# assign tes_ids to isoforms
message("Assign TES to isoforms")
ii <- findOverlaps(tes.bins, tes.base, maxgap = tes.window - 1)
tes.bins.annot <-
GenomicRanges::makeGRangesFromDataFrame(rbind(data.frame(tes.bins[S4Vectors::queryHits(ii)],
tes.base[S4Vectors::subjectHits(ii)])), keep.extra.columns = TRUE)
GenomicRanges::makeGRangesFromDataFrame(rbind(data.frame(
tes.bins[S4Vectors::queryHits(ii)],
tes.base[S4Vectors::subjectHits(ii)]
)), keep.extra.columns = TRUE)
tes.bins.annot <-
tes.bins.annot %>% dplyr::mutate(transcript_id = transcript_id, tes_id =count) %>%
tes.bins.annot %>%
dplyr::mutate(transcript_id = transcript_id,
tes_id = count) %>%
plyranges::select(gene_id, transcript_id, tes_id)
bins$tes.bins <- tes.bins
bins$tes.base <- tes.base
# create link database
linksDbs <- dplyr::left_join(as.data.frame(tes.bins.annot),
as.data.frame(tss.bins.annot),
by = "transcript_id") %>%
dplyr::select(gene_id.x, transcript_id, promoter_id, tes_id) %>% dplyr::rename(gene_id = gene_id.x) %>%
dplyr::mutate(pairs_id = paste(promoter_id, gsub(".*:", "", tes_id), sep =":"))
message("Create TSS/TES links database")
linksDbs <- dplyr::left_join(
as.data.frame(tes.bins.annot),
as.data.frame(tss.bins.annot),
by = "transcript_id"
) %>%
dplyr::select(gene_id.x, transcript_id, promoter_id, tes_id) %>%
dplyr::rename(gene_id = gene_id.x) %>%
dplyr::mutate(pairs_id = paste(promoter_id, gsub(".*:", "", tes_id), sep = ":"))
# Classify promoter type and utr type
# sorted with proximal first distal later
# output: class all 3'end isoforms
le.sort <- strandSort(le)
tt <- linksDbs %>% dplyr::group_by(gene_id) %>%
tt <- linksDbs %>%
dplyr::group_by(gene_id) %>%
dplyr::mutate(
utr_type = dplyr::case_when(
tes_id == min(tes_id) ~ "proximal",
tes_id == max(tes_id) ~ "distal",
TRUE ~ "other"
)
)
tt <- tt %>% group_by(gene_id) %>%
tt <- tt %>%
group_by(gene_id) %>%
dplyr::mutate(
promoter_type = case_when(
promoter_id == min(promoter_id) ~ "distal",
Expand All @@ -130,10 +161,17 @@ prepareLinksDatabase <- function(annotation, tss.window, tes.window) {
)
# classify APA-ATSS genes
# genes with more than 1 promoter different promoter
atss.gene <- tt %>% dplyr::distinct(promoter_id, .keep_all = TRUE) %>%
dplyr::group_by(gene_id) %>% dplyr::filter(dplyr::n() > 1) %>% dplyr::pull(gene_id)
apa.gene <- tt %>% dplyr::distinct(tes_id, .keep_all = TRUE) %>%
dplyr::group_by(gene_id) %>% dplyr::filter(dplyr::n() > 1) %>% dplyr::pull(gene_id)
message("Classify genes")
atss.gene <- tt %>%
dplyr::distinct(promoter_id, .keep_all = TRUE) %>%
dplyr::group_by(gene_id) %>%
dplyr::filter(dplyr::n() > 1) %>%
dplyr::pull(gene_id)
apa.gene <- tt %>%
dplyr::distinct(tes_id, .keep_all = TRUE) %>%
dplyr::group_by(gene_id) %>%
dplyr::filter(dplyr::n() > 1) %>%
dplyr::pull(gene_id)
tt <-
tt %>% dplyr::mutate(
tss.status = ifelse(gene_id %in% atss.gene, "ATSS", "single_promoter"),
Expand All @@ -147,26 +185,34 @@ prepareLinksDatabase <- function(annotation, tss.window, tes.window) {
tt <- subset(tt, gene_id == promoter_gene)
tt$promoter_gene <- NULL
bins$links <- tt
tt <- tt %>% dplyr::group_by(gene_id) %>%
tt <- tt %>%
dplyr::group_by(gene_id) %>%
dplyr::mutate(
utr_type = dplyr::case_when(
tes_id == min(tes_id) ~ "proximal",
tes_id == max(tes_id) ~ "distal",
TRUE ~ "other"
)
)
tt <- tt %>% group_by(gene_id) %>%
tt <- tt %>%
group_by(gene_id) %>%
dplyr::mutate(
promoter_type = case_when(
promoter_id == min(promoter_id) ~ "distal",
promoter_id == max(promoter_id) ~ "proximal",
TRUE ~ "intermediate"
)
)
atss.gene <- tt %>% dplyr::distinct(promoter_id, .keep_all = TRUE) %>%
dplyr::group_by(gene_id) %>% dplyr::filter(dplyr::n() > 1) %>% dplyr::pull(gene_id)
apa.gene <- tt %>% dplyr::distinct(tes_id, .keep_all = TRUE) %>%
dplyr::group_by(gene_id) %>% dplyr::filter(dplyr::n() > 1) %>% dplyr::pull(gene_id)
atss.gene <- tt %>%
dplyr::distinct(promoter_id, .keep_all = TRUE) %>%
dplyr::group_by(gene_id) %>%
dplyr::filter(dplyr::n() > 1) %>%
dplyr::pull(gene_id)
apa.gene <- tt %>%
dplyr::distinct(tes_id, .keep_all = TRUE) %>%
dplyr::group_by(gene_id) %>%
dplyr::filter(dplyr::n() > 1) %>%
dplyr::pull(gene_id)
tt <-
tt %>% dplyr::mutate(
tss.status = ifelse(gene_id %in% atss.gene, "ATSS", "single_promoter"),
Expand All @@ -178,6 +224,6 @@ prepareLinksDatabase <- function(annotation, tss.window, tes.window) {
result$TESCoordinate.base <- tes.base
result$TSSCoordinate.bins <- tss.bins
result$TSSCoordinate.base <- tss.base
message("Database Sucessfully created")
return(result)
}