plot-methods {casper} | R Documentation

## Plot estimated read start and fragment length distributions.

### Description

Plots the estimated fragment length (insert size) distribution and the relative read start distribution (0 indicating transcription start, 1 transcription end). The former checks that the insert size distribution matches that described in the experimental protocol. The latter checks the extent to which reads are non-uniformly distributed (note: casper does NOT assume reads to be uniformly distributed, so a lack of uniformity is not a problem per se).

### Arguments

`x` | Object of type `readDistrs`, as returned by `getDistrs`.
`y` | Set to `"fragLength"` to plot the estimated insert size ditribution. Set to `"readSt"` to plot a histogram of the estimated read start distribution.
`...` | Further arguments to be passed on to plot.

### Methods

`signature(x = "readDistrs", y = "ANY")`

  `x` is an object of type `readDistrs`, as returned by `getDistrs`. The plot allows to visualize the fragment length and read start distributions in a given sample.

`signature(x = "readDistrs")`

  `x` is an object of type `readDistrs`, as returned by `getDistrs`. The plot allows to visualize the fragment length and read start distributions in a given sample.

`signature(x = "readDistrsList", y = "ANY")`

  `x` is an object of type `readDistrsList` storing fragment length and read start distributions for multiple samples.

`signature(x = "readDistrsList")`

  `x` is an object of type `readDistrsList` storing fragment length and read start distributions for multiple samples.

### Examples

    #See getDistrs examples

[Package casper version 2.14.0 Index]