This is an S3 generic. valr includes methods to coerce tbl_df and GRanges objects.
as.tbl_interval(x) # S3 method for tbl_df as.tbl_interval(x) # S3 method for data.frame as.tbl_interval(x) # S3 method for GRanges as.tbl_interval(x)
x | object to convert to tbl_interval. |
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# NOT RUN { gr <- GenomicRanges::GRanges( seqnames = S4Vectors::Rle( c("chr1", "chr2", "chr1", "chr3"), c(1, 1, 1, 1)), ranges = IRanges::IRanges( start = c(1, 10, 50, 100), end = c(100, 500, 1000, 2000), names = head(letters, 4)), strand = S4Vectors::Rle( c("-", "+"), c(2, 2)) ) as.tbl_interval(gr) # There are two ways to convert a tbl_interval to GRanges: gr <- GenomicRanges::GRanges( seqnames = S4Vectors::Rle(x$chrom), ranges = IRanges::IRanges( start = x$start + 1, end = x$end, names = x$name), strand = S4Vectors::Rle(x$strand) ) # or: gr <- GenomicRanges::makeGRangesFromDataFrame(dplyr::mutate(x, start = start +1)) # }