seedRegions: A function to retrieve the seed regions from microRNA...
In microRNA: Data and functions for dealing with microRNAs

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/seedReg.R

The seed region of a microRNA consists of a set of nucleotides at the 5' end of the microRNA, typically bases 2 through 7, although some times 8 is used.

1	seedRegions(x, start = 2, stop = 7)

`x`	A vector of microRNA sequences.
`start`	The start locations, can be a vector.
`stop`	The stop locations, can be a vector.

We use substr to extract these sequences.

A vector of the same length as x with the substrings.

R. Gentleman

substr

1
2
3

 data(hsSeqs)
 seedRegions(hsSeqs[1:5])
 seedRegions(hsSeqs[1:3], start=c(2,1,2), stop=c(8,7,9))

hsa-let-7a hsa-let-7b hsa-let-7c hsa-let-7d hsa-let-7e 
  "GAGGUA"   "GAGGUA"   "GAGGUA"   "GAGGUA"   "GAGGUA" 
hsa-let-7a hsa-let-7b hsa-let-7c 
 "GAGGUAG"  "UGAGGUA" "GAGGUAGU"