aee: Ancestral Transcriptome State Inference

In jingwyang/AnceTran: the R package for analyzing TF-binding evolution based on ChIP-seq data

Description

This function is to inference ancestral transcriptome state and related statistical uncertainty based on RNA-seq expression data or ChIP-seq TF-binding data.

Usage

aee(x, phy, mat, select = c("descendents", "all"), CI = TRUE)

Arguments

x	a vector of known expression or TF binding score values of genes, preferably log2-transformed
phy	a phylogenetic tree in the form of object "phylo"
mat	a matrix generated from "varMatInv" function
select	indicate if descendents of the node or all tips should be used
CI	a logical specifying whether to return the 95 of the estimated ancestral transcriptome value.

Value

returns a list containing estimated ancestral transcriptome states as well as other requested parameters

jingwyang/AnceTran documentation built on May 19, 2019, 2:57 a.m.