From tabular data to Genomic Ranges
In the video, you learned ways to create GRanges
objects. You can define a GRange with a range's name, start, and end positions (seqnames
, start
, and end
). If you have data in table format, you can also transform it into a GRanges
object. Let's use a data frame, called seq_intervals
, as this is most likely where you have stored your sequence intervals. Note: you can also use a tibble
if you are more familiar with them.
You will use the predefined seq_intervals
data frame to transform into a GRanges
object using the as()
function. The as()
function was introduced in the last video - it takes in an object and the name of the class to convert the object to.
This exercise is part of the course
Introduction to Bioconductor in R
Exercise instructions
- Load
GenomicRanges
. - Print
seq_intervals
to see how it looks. - Transform
seq_intervals
into aGRanges
object, call the new objectmyGR
. - Print
myGR
.
Hands-on interactive exercise
Have a go at this exercise by completing this sample code.
# Load GenomicRanges package
library(GenomicRanges)
# Print seq_intervals
___
# Create myGR
___ <- ___(___, "___")
# Print myGR
___