utr_count: Count number of occurence of DNA substring in UTR regions

In CharlesJB/mirnatools: A package to manage miRNA sequencing data

Description

This function will look for the number of occurence of every substrings of length substring_length in the UTR regions of a given genome.

Usage

utr_count(sequence_name, sequence, substring_length, genome, utr,
  reverse_complement = FALSE)

Arguments

sequence_name	A character vector of length 1 corresponding to name of the current sequence being analysed.
sequence	A character vector or a DNAString object corresponding to the miRNA sequence to analyze.
substring_length	The length of each substring to use to find perfect matches in the UTR regions.
utr	Which UTR region to use? "5UTR", "3UTR" or "both". Default: "5UTR".
reverse_complement	Use the reverse complement of the sequence? Default: FALSE.

Value

A data.frame with the following columns:

• name The sequence_name argument value.

• sequence The sequence argument value.

• substring The current_substring.

• substring The position of the substring in the sequence.

• count The number of perfect matches for the substring in the UTR regions.

• percent The percentage of all the possible substrings of substring_length that have a smaller number of perfect matches in the UTR regions.

• mirbase_count The number of perfect matches for the all the miRBase substrings at the same position of its respective sequence in the specified genome.

• mirbase_percent The percentage of all miRBase substrings at the same position in its respective sequence that have a smaller number of perfect matches in the UTR region of the specified genome.

• reverse_complement The value of the reverse complement argument.

CharlesJB/mirnatools documentation built on May 6, 2019, 9:58 a.m.