predictNMI: Neuron Maturity Index (NMI) estimation

In maplesword/neuMatIdx: neuMatIdx: Neuron Maturity Index

Description

Taking gene expressions of neuron samples (in FPKM), this function predicts the Neuron Maturity Index (NMI) which is an estimate of degree of neuron maturation. The Index ranges between 0 and 1. The more it is close to one, the more mature the neuron sample is. The models were trained using the mature and immature neuron single cell RNA-seq data in Darmanis, et al. PNAS, 2015.

Usage

predictNMI(fpkm, standardize = TRUE, returnFpkmStd = FALSE)

Arguments

fpkm	A matrix of gene expression represented by FPKM. Each row represent one gene (named by EnsemblID) and each column represent one sample
standardize	To determine whether standardization should be applied to fpkm matrix first
returnFpkmStd	To determine whether the standardlized FPKM of samples should be returned.

Value

A list with at least two components. The first component (modularNMI) is a matrix of modular NMI, with 109 columns each of which shows NMI of one module. The second component (overallNMI) is a matrix of overall NMI, with three columns representing NMI-all, NMI-discriminable and Neuron Activity Index (NAI). The third element is a matrix of standardized FPKM if returnFpkmStd is TRUE.

maplesword/neuMatIdx documentation built on May 31, 2019, 1:16 p.m.