GenomicRanges package (Genomic ranges)

Create a GRanges object using the following information:

chr = c("chr1","chr1", "chr2")
start = c(10000, 11100, 200000)
end = c(10300, 11500, 200300)
strand = c("+", "-", "-")
score = c(10,20,15)

Use the start(), end(), strand(), seqnames() and width() functions on the GRanges object you created. What information do you obtain?

Add the width of ranges as a metadata column named dimension.
Hint: use $ as if it is a dataframe.

Extract metadata columns.

Create a subset of the GRanges object containing only intervals on the + strand and another subset with intervals located on chr1.
Hint: GRanges objects can be subset using the [ ] operator, similar to data frames.
However, you may need to use start(), end(), strand(), and seqnames() within [ ].

Modify the chromosome of the second interval in the GRanges object to chr20.

Try creating a GRanges object using the following data:

seqnames = c("chr4", "chr6", "chr9", "chr22")
start = c(1, 679, 7000)
end = c(7, 666, 34000)

Are you able to create it successfully? Why or why not?

Create a GRanges object using the following data:

seqnames = c("chr4", "chr6", "chr9", "chr22")
start = c(1, 679, 7000, 999)
end = c(7, 6666, 34000, 1000)

Assign names to the GRanges object you created: Sequence1, Sequence2, Sequence3, and Sequence4.

Extract the range named Sequence3 from the GRanges object.