intercompare: Compare gene elongation rates between 2 different conditions

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

Compare gene elongation rates between 2 different conditions

Description

Compare gene elongation rate difference for each gene between 2 different conditions. For each condition, if the number of replicates is < 3, Fisher's test will be used to calculate the p-values and adjusted p-values of the rate differences, while if the number of replicates is >= 3, Wilcox test and limma will be used to calculate 2 sets of p-values and adjusted p-values (Wilcox test based and limma based).

Usage

intercompare(inferresmat, groupnames)

Arguments

inferresmat	A data.frame recording the elongation rates for the genes in different conditions. Can be generated using the function orgintercompareinput.
groupnames	A vector with the elements corresponding to the condition names of the rate columns in the data.frame indicated by the parameter inferresmat.

Value

A data.frame with one row for one gene and the columns are the average transcription elongation rates for each condition (log2 transformed), the log2FC, the p-value and adjusted p-value (adjusted by Benjamini & Hochberg method) of the difference.

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