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Add files via upload #8

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28 changes: 12 additions & 16 deletions CovertingCoordinates/openASO_position.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -46,7 +46,7 @@ genseq_byaso$transcript_id <- gsub("\\..*","",genseq_byaso$hg38.knownGene.name)


# make smol
genseq_byaso <- tail(genseq_byaso,1000)
# genseq_byaso <- head(genseq_byaso,1000)
```

### Map the transcriptomic coordinates
Expand Down Expand Up @@ -81,22 +81,17 @@ aso_txt_pos <- na.omit(aso_txt_pos, cols = "start")
# convert the transcript position information into an IRanges format.
# add an ASO group number 'aso_grp' to be able to connect two genome ranges corresponding to the same ASO, but spanning exons.

# grp_list <- lapply(aso_txt_pos, function(x){lapply(x, row.names)})
# grp_list <- lapply(aso_txt_pos, function(x){lapply(x, row.names); x})

# ir <- IRanges(start = aso_txt_pos$start, width = (aso_txt_pos$end - aso_txt_pos$start), names = aso_txt_pos$transcript_id, aso_grp = rownames(aso_txt_pos))

ir <- IRanges(start = aso_txt_pos$start, width = (aso_txt_pos$end - aso_txt_pos$start), names = aso_txt_pos$transcript_id, aso_grp = list(rownames(aso_txt_pos)))

# create an EnsDB object containing genomic position information.
dbfile <- system.file("extdata/EnsDb.Hsapiens.v86.sqlite", package = "EnsDb.Hsapiens.v86")
db <- EnsDb(dbfile)

# latest version of X.toGenome tries to replace id with a group identifier. Defaults to using 'NAMES'/transcript id which is not unique enough to join back at the very end.
# latest version of X.toGenome tries to replace id with a group identifier. Defaults to using 'NAMES' transcript id which is not unique enough to join back at the very end.

# gr <- transcriptToGenome(ir, db)
gr <- transcriptToGenome(ir, db)
# gr <- transcriptToGenome(ir, db, id = mcols(ir)[,1])
gr <- transcriptToGenome(ir, db, id = mcols(ir)$aso_grp)
# gr <- transcriptToGenome(ir, db, id = mcols(ir)$aso_grp)

```

Expand All @@ -107,9 +102,9 @@ gr <- transcriptToGenome(ir, db, id = mcols(ir)$aso_grp)
# unlist the GRanges object to be able to pull transcript start/end information without direct reference to transcript.
gr_unlist <- unlist(gr, recursive = TRUE, use.names = TRUE)

gnm_df <- data.frame(loci = seqnames(gr_unlist),
starts = start(gr_unlist) - 1,
ends = end(gr_unlist),
gnm_df <- data.frame(chrom = seqnames(gr_unlist),
chromStart = start(gr_unlist),
chromEnd = end(gr_unlist) + 1,
strand = strand(gr_unlist),
gr_unlist@ranges@width,
gr_unlist@elementMetadata@listData[["tx_id"]], gr_unlist@elementMetadata@listData[["tx_start"]], gr_unlist@elementMetadata@listData[["tx_end"]])
Expand All @@ -128,13 +123,14 @@ colnames(gnm_df)[colnames(gnm_df) ==

```{r GRanges to BED format, warning = FALSE}
# create new data frame that connects ASO info to generated genome range info.

final_df <- dplyr::full_join(aso_txt_pos, gnm_df, by = c('transcript_id' = 'tx_id', 'start' = 'tx_start', 'end' = 'tx_end', ))
df <- merge(aso_txt_pos, gnm_df, by.x = c('transcript_id', 'start'), by.y = c('tx_id', 'tx_start'))

# add a unique identifier
final_df$uniq_id <- paste(final_df$GeneID, "_", final_df$ASOseq)
df$uniq_id <- paste(df$GeneID, "_", df$ASOseq)

# convert the data frame to bed format.
# reorder columns to match BED format.
col_order <- c("chrom", "chromStart", "chromEnd", "uniq_id", "transcript_id", "ASOseq", "aso_rc_seq", "ASOeffective","strand","start", "end", "tx_end", "width", "GeneID", "OriginalName", "HGNC.ID", "hg38.knownGene.name", "Sequence")
final_df <- df[ , col_order]

# write.csv(final_df, file = "openASO_gr.bed", quote = F, sep = "\t", row.names = F, col.names = F)
```
Expand Down