as_iranges {plyranges} | R Documentation |
The as_i(g)ranges function looks for column names in .data called start, end, width, seqnames and strand in order to construct an IRanges or GRanges object. By default other columns in .data are placed into the mcols ( metadata columns) slot of the returned object.
as_iranges(.data, ..., keep_mcols = TRUE) as_granges(.data, ..., keep_mcols = TRUE)
.data |
a |
... |
optional named arguments specifying which the columns in .data containin the core components a Ranges object. |
keep_mcols |
place the remaining columns into the metadata columns slot (default=TRUE) |
a Ranges object.
df <- data.frame(start=c(2:-1, 13:15), width=c(0:3, 2:0)) as_iranges(df) df <- data.frame(start=c(2:-1, 13:15), width=c(0:3, 2:0), strand = "+") # will return an IRanges object as_iranges(df) df <- data.frame(start=c(2:-1, 13:15), width=c(0:3, 2:0), strand = "+", seqnames = "chr1") as_granges(df) # as_g/iranges understand alternate name specification df <- data.frame(start=c(2:-1, 13:15), width=c(0:3, 2:0), strand = "+", chr = "chr1") as_granges(df, seqnames = chr) # can also handle DFrame input df <- methods::as(df, "DFrame") df$y <- IRanges::IntegerList(c(1,2,3), NA, 5, 6, 8, 9, 10:12) as_iranges(df) as_granges(df, seqnames = chr)