A function to retrieve the seed regions from microRNA sequences

Description

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.

Usage

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

Arguments

Details

We use substr to extract these sequences.

Value

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

Author(s)

R. Gentleman

See Also

substr

Examples

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

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
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Type 'license()' or 'licence()' for distribution details.

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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(microRNA)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/microRNA/seedRegions.Rd_%03d_medium.png", width=480, height=480)
> ### Name: seedRegions
> ### Title: A function to retrieve the seed regions from microRNA sequences
> ### Aliases: seedRegions
> ### Keywords: manip
> 
> ### ** Examples
> 
>  data(hsSeqs)
>  seedRegions(hsSeqs[1:5])
hsa-let-7a hsa-let-7b hsa-let-7c hsa-let-7d hsa-let-7e 
  "GAGGUA"   "GAGGUA"   "GAGGUA"   "GAGGUA"   "GAGGUA" 
>  seedRegions(hsSeqs[1:3], start=c(2,1,2), stop=c(8,7,9))
hsa-let-7a hsa-let-7b hsa-let-7c 
 "GAGGUAG"  "UGAGGUA" "GAGGUAGU" 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>