distances: Internal functions for estimating pair-wise expression...

In hr1912/phyExp: the R package for analyzing expression evolution based on RNA-seq data

Description

Several published methods to estimate pair-wise expression distances

Usage

dist.nbdln(reads.count = NULL, gene_length = NULL, omega = NULL)

dist.u(reads.count = NULL, gene_length = NULL)

dist.jsd(expMat = NULL)

dist.pea(expMat = NULL)

dist.spe(expMat = NULL)

dist.euc(expMat = NULL)

dist.cos(expMat = NULL)

dist.tani(expMat = NULL)

dist.jac(expMat = NULL)

dist.ced(expMat = NULL)

dist.sou(expMat = NULL)

References

Chen H, He X. 2016. The Convergent Cancer Evolution toward a Single Cellular Destination. Mol Biol Evol 33:4-12

Gu X, Su Z. 2007. Tissue-driven hypothesis of genomic evolution and sequence-expression correlations. Proc Natl Acad Sci USA 104:2779-2784.

Pereira V, Waxman D, Eyre-Walker A. 2009. A problem with the correlation coefficient as a measure of gene expression divergence. Genetics 183:1597-1600.

Sudmant PH, Alexis MS, Burge CB. 2015. Meta-analysis of RNA-seq expression data across species, tissues and studies. Genome Biol 16:287.

Distance based on negative bio distribution and log normal model

hr1912/phyExp documentation built on July 13, 2019, 5:18 p.m.