Sequence Ranges

Introduction to Bioconductor in R

Paula Andrea Martinez, PhD.

Data scientist

IRanges with numeric arguments

# Loading IRanges
library(IRanges)

A range is defined by start and end

myIRanges <- IRanges(start = 20, end = 30)
myIRanges

IRanges object with 1 range and 0 metadata columns:
   start       end     width
<integer> <integer> <integer>
[1]   20        30        11

(myIRanges_width <- IRanges(start = c(1, 20), width = c(30, 11)))

 IRanges object with 2 ranges and 0 metadata columns:
         start       end     width    
      <integer> <integer> <integer>
[1]         1        30        30       
[2]        20        30        11

(myIRanges_end <- IRanges(start = c(1, 20), end = 30))

 IRanges object with 2 ranges and 0 metadata columns:
         start       end     width    
      <integer> <integer> <integer>
[1]         1        30        30       
[2]        20        30        11

Equation: width = end - start + 1

Rle - run length encoding

Rle stands for Run length encoding
Computes and stores the lengths and values of a vector or factor
Rle is general S4 container used to save long repetitive vectors efficiently

(some_numbers <- c(3, 2, 2, 2, 3, 3, 4, 2))

3 2 2 2 3 3 4 2

(Rle(some_numbers))

numeric-Rle of length 8 with 5 runs
Lengths: 1 3 2 1 1
Values : 3 2 3 4 2

IRanges with logical vector

IRanges(start = c(FALSE, FALSE, TRUE, TRUE))

 IRanges object with 1 range and 0 metadata columns:
      start       end     width
  <integer> <integer> <integer>
[1]       3         4         2

IRanges with logical Rle

gi <- c(TRUE, TRUE, FALSE, FALSE, TRUE, TRUE, TRUE)
myRle <- Rle(gi)

logical-Rle of length 7 with 3 runs
Lengths:     2     2     3
Values :  TRUE FALSE  TRUE

IRanges(start = myRle)

IRanges object with 2 ranges and 0 metadata columns:
         start       end     width
      <integer> <integer> <integer>
[1]         1         2         2
[2]         5         7         3

In summary

IRanges are hierarchical data structures can contain metadata.

To construct IRanges objects:

start, end, or width as numeric vectors (or NULL).
start argument as a logical vector or logical Rle object.
- Rle stands for Run length encoding and is storage efficient.
- IRanges arguments get recycled (fill in the blanks).
- equation for sequence range: width = end - start + 1.

Let's practice using sequence ranges!

Introduction to Bioconductor in R