empirical_density


Empirical fragment length distribution was estimated using 7
  randomly selected RNA-seq samples from the GEUVADIS dataset ('t Hoen et
  al 2013). One sample was selected from each of the 7 laboratories that
  performed the sequencing. We used Picard's "CollectInsertSizeMetrics" tool
  (http://broadinstitude.github.io/picard/), version 1.121, to estimate
  the fragment size distribution based on read alignments. Code we used
  to estimate this distribution is available at
  <a href="https://github.com/alyssafrazee/polyester/blob/master/make_fraglen_model.R">https://github.com/alyssafrazee/polyester/blob/master/make_fraglen_model.R</a>.


This package can be used to simulate RNA-seq reads from
differential expression experiments with replicates. The reads can then be
aligned and used to perform comparisons of methods for differential
expression.

Alyssa Frazee

polyester

Simulate RNA-seq reads

empirical_density function

<code>logspline</code> object (created with <code><a rd-options="" href="/link/logspline?package=polyester&version=1.6.0" data-mini-rdoc="polyester::logspline">logspline</a></code>)
  specifying the empirical density of fragment lengths in the 7 GEUVADIS
  samples.

Format


Empirical fragment length distribution was estimated using 7
  randomly selected RNA-seq samples from the GEUVADIS dataset ('t Hoen et
  al 2013). One sample was selected from each of the 7 laboratories that
  performed the sequencing. We used Picard's "CollectInsertSizeMetrics" tool
  (http://broadinstitude.github.io/picard/), version 1.121, to estimate
  the fragment size distribution based on read alignments. Code we used
  to estimate this distribution is available at
  <a href = 'https://github.com/alyssafrazee/polyester/blob/master/make_fraglen_model.R'>https://github.com/alyssafrazee/polyester/blob/master/make_fraglen_model.R</a>.


<code>logspline</code> object (created with <code><a rd-options='' href='logspline'>logspline</a></code>)
  specifying the empirical density of fragment lengths in the 7 GEUVADIS
  samples.

empirical_density: Estimated distribution of fragment lengths

Description

Arguments

Format

References