intracompare: Divide genes into different quantile groups according to...

In yuabrahamliu/proRate: proRate is an R package to infer gene transcription rates with a novel least sum of squares method.

Divide genes into different quantile groups according to their rates

Description

Divide genes into different quantile groups according to their rates inferred from the calrate function, or mcalrate function.

Usage

intracompare(inferres, targetgenes = NULL, quantilenum = 4)

Arguments

inferres	The result list generated by the calrate function or mcalrate function.
targetgenes	Which genes need to be divided into quantile groups. If it is NULL (The default value), all genes provided by the parameter inferres will be analyzed. If its value is 'significant', only genes judged as significant genes by calrate or mcalrate will be analyzed. While the the value of this parameter can also be a vector with gene symbols as elements and only genes covered by this vector will be analyzed.
quantilenum	How many quantile groups need to be divided. Default value is 4.

Value

A list with 2 data.frames as elements. One of them records the absolute elongation rates of the genes (bp/min) and divide the genes into several quantile groups with genes in quantile1 group having the lowest rates. The other data.frame records the relative elongation rates of the genes (percent of gene body/min) and divide them into quantile groups. If the value of parameter inferres is from mcalrate, the absolute and relative rates of the genes are the mean of all the Pro-seq or Gro-seq pairs.

yuabrahamliu/proRate documentation built on Nov. 3, 2024, 10:14 a.m.