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Using GRanges with ExonR

GRanges is a very useful package for working with genomic ranges in R.

Loading the Data​

To get started we need something to work with, and that's where we see ExonR for the first time. We can load an example gzip GFF file from S3 with as such:

> library(exonr)

# Load the GFF file
> rdr <- read_gff_file("s3://wtt-01-dist-prd/gffs/Ga0604745_crt.gff")
> df <- as.data.frame(rdr)

Creating a GRanges Object​

Now that there's a data frame, we can create a GRanges object from it.

> library(GenomicRanges)

> gr <- GRanges(seqnames = df$seqname,
                ranges = IRanges(start = df$start, end = df$end))

> gr
GRanges object with 17289 ranges and 0 metadata columns:
                  seqnames    ranges strand
                     <Rle> <IRanges>  <Rle>
      [1] Ga0604745_000026         1      *
      [2] Ga0604745_000026         1      *
      [3] Ga0604745_000026        73      *
      [4] Ga0604745_000026       147      *
      [5] Ga0604745_000026       219      *
      ...              ...       ...    ...
  [17285] Ga0604745_216712       159      *
  [17286] Ga0604745_216719        10      *
  [17287] Ga0604745_216719        10      *
  [17288] Ga0604745_216719        84      *
  [17289] Ga0604745_216719       157      *
  -------
  seqinfo: 1664 sequences from an unspecified genome; no seqlengths