cdnaf


This positional bias model was estimated in Li and Jiang (2012).
  With cDNA fragmentation, reads are more likely to have come from the 3'
  end of the transcript. The probabilities included in this dataset were
  estimated from Supplementary Figure S3 in Li and Jiang's manuscript.
  Data points from the figure were inferred and exported as CSV files
  using WebPlotDigitizer. The CSV files and the code used to process them
  and create the datasets are available in the Polyester GitHub
  repository (<a href="https://github.com/alyssafrazee/polyester">https://github.com/alyssafrazee/polyester</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

cdnaf function

data frame with 100 rows and 2 columns. Column 1 is position along a
  transcript (in percent), while Column 2 is the probability of getting a
  fragment at that position. Column 2 sums to 1.

Format


This positional bias model was estimated in Li and Jiang (2012).
  With cDNA fragmentation, reads are more likely to have come from the 3'
  end of the transcript. The probabilities included in this dataset were
  estimated from Supplementary Figure S3 in Li and Jiang's manuscript.
  Data points from the figure were inferred and exported as CSV files
  using WebPlotDigitizer. The CSV files and the code used to process them
  and create the datasets are available in the Polyester GitHub
  repository (<a href = 'https://github.com/alyssafrazee/polyester'>https://github.com/alyssafrazee/polyester</a>).


cdnaf: Model of positional bias that can arise when RNA-seq is performed using protocols relying on cDNA fragmentation.

Description

Arguments

Format

References