computeNoiseForSubset: Select a random subset of data for noise estimation.

In noise: Estimation of Intrinsic and Extrinsic Noise from Single-Cell Data

Description

This function randomly selects a subset of cells (rows) from the data set, computes multiple estimates of intrinsic and extrinsic noise, as well as their mean and standard deviation.

Usage

computeNoiseForSubset(data, sample.size, n.iter)

Arguments

data	A numeric matrix of two columns. Each row is a cell, and each column expression of a reporter gene.
sample.size	An integer that specifies the number of cells in the subset.
n.iter	An integer that specifies the number of iterations (for calcuation of mean and standard deviation).

Value

A list that consists of the following components:

intrinsic	A numeric matrix of esimated intrinsic noise. 7 rows and n.iter columns.
extrinsic	A numeric matrix of esimated extrinsic noise. 4 rows and n.iter columns.
intrinsic.mean	A numeric vector of length 7 that contains the mean estimates of intrinsic noise.
intrinsic.sd	A numeric vector of length 7 that contains the standard deviation of the estimates of intrinsic noise.
extrinsic.mean	A numeric vector of length 7 that contains the mean estimates of extrinsic noise.
extrinsic.sd	A numeric vector of length 7 that contains the standard deviation of the estimates of extrinsic noise.

Author(s)

Audrey Q. Fu

References

Fu, A. Q. and Pachter, L. (2016). Estimating intrinsic and extrinsic noise from single-cell gene expression measurements. arXiv:1601.03334.

See Also

computeIntrinsicNoise, computeExtrinsicNoise, elowitz_data, yang_nl10.

Examples

data(yang_nl10)

# quantile normalization on log2 transformed data
# install bioconductor package for quantile normalization
# source('http://bioconductor.org/biocLite.R')
# biocLite('preprocessCore')
library(preprocessCore)

# ignore a few values that are negative
yang_nl10.pos <- yang_nl10[-which (yang_nl10[,1]<0),]
yang_nl10.pos.log2.quant <- normalize.quantiles (as.matrix (log2 (yang_nl10.pos[,c(1,3)])))

# subset the data and compute noise estimates
yang.50 <- computeNoiseForSubset (yang_nl10.pos.log2.quant, sample.size=50, n.iter=1000)
summary (yang.50)

Example output

               Length Class  Mode   
intrinsic      7000   -none- numeric
extrinsic      4000   -none- numeric
intrinsic.mean    7   -none- numeric
intrinsic.sd      7   -none- numeric
extrinsic.mean    4   -none- numeric
extrinsic.sd      4   -none- numeric

noise documentation built on Jan. 8, 2021, 2:04 a.m.