plot-methods: Plot estimated read start and fragment length distributions.

In casper: Characterization of Alternative Splicing based on Paired-End Reads

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

casper documentation built on Dec. 17, 2020, 2:01 a.m.