Description Usage Arguments Value Author(s) References See Also Examples

View source: R/computeNoiseForSubset.R

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.

1 | ```
computeNoiseForSubset(data, sample.size, n.iter)
``` |

`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). |

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. |

Audrey Q. Fu

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

`computeIntrinsicNoise`

, `computeExtrinsicNoise`

, `elowitz_data`

, `yang_nl10`

.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 | ```
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)
``` |

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.