generate_fragments: generate a set of fragments from a set of transcripts

In alyssafrazee/polyester-release: Simulate RNA-seq reads

Description

Convert each sequence in a DNAStringSet to a "fragment" (subsequence)

Usage

generate_fragments(tObj, fraglen, fragsd = 25)

Arguments

tObj	DNAStringSet of sequences from which fragments should be extracted
fraglen	Mean fragment length.
fragsd	Standard deviation of fragment length. Fragment lengths are drawn from a normal distribution with mean fraglen and standard deviation fragsd.

Value

DNAStringSet consisting of one randomly selected subsequence per element of tObj.

Examples

library(Biostrings)
  data(srPhiX174)
  set.seed(174)
  srPhiX174_fragments = generate_fragments(srPhiX174, fraglen=15, fragsd=3)
  srPhiX174_fragments
  srPhiX174

alyssafrazee/polyester-release documentation built on May 12, 2019, 2:32 a.m.