-
Notifications
You must be signed in to change notification settings - Fork 2
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
1 parent
7a5144c
commit e1411a4
Showing
4 changed files
with
111 additions
and
0 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,53 @@ | ||
#' Split a seqlevel in two pieces | ||
#' | ||
#' For scaffolding or plotting purposes, it may be useful to split some | ||
#' sequences into smaller ones. | ||
#' | ||
#' @note This function only splits at breakpoints. | ||
#' | ||
#' @param gb A `GBreaks` object. | ||
#' @param seq A one seqlevel from `gr` | ||
#' @param bp The breakpoint where to split. | ||
#' | ||
#' @returns Returns a modified `GRanges` object in which the sequence has been | ||
#' split Its [`seqinfo`] has a new entry for the new levels, and the old | ||
#' level is not removed. If no `seqlengths` were present in the original | ||
#' object, they are arbitrarily set as the maximal end value for each `seqlevel`. | ||
#' | ||
#' @examples | ||
#' splitSeqLevel(exampleInsertion, "chrA", 200) | ||
#' | ||
#' @family modifier functions | ||
#' @family scaffolding functions | ||
#' | ||
#' @author Charles Plessy | ||
#' | ||
#' @include guessSeqLenghts.R | ||
#' | ||
#' @export | ||
|
||
splitSeqLevel <- function(gb, seq, bp) { | ||
# Isolate the target ranges that are in the selected seqlevel. | ||
gbl.all <- split(gb, seqnames(gb)) | ||
gb <- gbl.all[[seq]] | ||
|
||
# Prepare new levels and lengths | ||
seq_1 <- paste0(seq, "_1") | ||
seq_2 <- paste0(seq, "_2") | ||
seqlevels(gb) <- c(seqlevels(gb), seq_1, seq_2) | ||
seqlengths(gb)[seq_1] <- bp | ||
seq_length <- seqlengths(gb)[[seq]] | ||
if(is.na(seq_length)) seq_length <- guessSeqLengths(gb)[[seq]] | ||
seqlengths(gb)[seq_2] <- seq_length - bp | ||
genome(gb)[c(seq_1, seq_2)] <- unique(genome(gbl.all)) | ||
|
||
# Split, change, merge | ||
gbl <- split(gb, ifelse(end(gb) <= bp, seq_1, seq_2)) | ||
seqnames(gbl[[seq_1]]) <- factor(seq_1, levels = seqlevels(gb)) | ||
gbl[[seq_2]] <- shift(gbl[[seq_2]], - bp) | ||
seqnames(gbl[[seq_2]]) <- factor(seq_2, levels = seqlevels(gb)) | ||
gbl.all[[seq]] <- unlist(gbl) | ||
|
||
# Return new GBreaks object | ||
sort(ignore.strand = TRUE, unlist(gbl.all)) | ||
} |
Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.
Oops, something went wrong.