miRNA.which.arm: Predict miRNA arm Predict which arm (3' or 5') of the...

In drmjc/genomics: Genomics related functions.

Description

Predict miRNA arm Predict which arm (3' or 5') of the precursor miRNA that the mature miR is on This uses purely the sequences of the precursor, and the mature miRNA.

Usage

  miRNA.which.arm(mature.seq, precursor.seq, THRESH = 0.44,
    detailed.alignment = NULL)

Arguments

mature.seq	a vector of N mature miRNA sequences
precursor.seq	a vector of N precursor miRNA sequences
THRESH	The alignment score (see notes) that distinguishes the 3'/5' arms
detailed.alignment	If you've already run miRNA.align.mir.to.miR, then you can provide this argument, instead of mature.seq and precursor.seq

Value

a vector of N values that can be either "5p" or "3p"

Note

Alignment score is the alignments' start index relative to the precursor divided by the length of the precursor

Author(s)

Mark Cowley, 2009-01-08

drmjc/genomics documentation built on May 15, 2019, 2:22 p.m.