Description Usage Arguments Value Examples

This function calculates log-fold changes, likelihood ratio test statistics, and p-values for a list of genes. This function should be called after a commom correlation matrix is returned by ‘correlationCoefficient’.

1 | ```
LRtest1(d,z,use.commonSigma,id)
``` |

`d` |
This is a PLNseq object. |

`z` |
J independent samples (a matrix of dimension J by R) drown from multivariate normal distribution with expectations 0, variances 1, and a common correlation coefficient matrix estimated by ‘correlationCoefficient’. |

`use.commonSigma` |
Use common ‘sigma’ (TRUE) or genewise ‘sigma’ (FALSE), with default value ‘FALSE’. |

`id` |
A vector consisting of a subset of 1,...,J, with default value 1:J (all genes are analyzed). |

`LR` |
Estimation and test results: ‘log-FC’, ‘LR statistic’, ‘p value’. |

1 2 3 4 5 6 7 8 9 10 11 12 13 | ```
data(lung);
count = lung[,c(2:4,8:10)];
d = PLNobject(count,conditionNumber=2);
d = sizeFactor(d,maxCount=2e3);
## Not run:
## d = commonSigma(d);
## d$commonCorrelation = TRUE;
## d = correlationCoefficient(d);
## d = genewiseSigma(d);
## library('MASS');
## z = mvrnorm(n=1e5,mu=rep(0,2),Sigma=d$rho);
## d = LRtest1(d,z,use.commonSigma=FALSE,id=1:100);
``` |

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