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 cluster-specific correlations are returned by ‘correlationCoefficient’.

1 | ```
LRtest2(d,M,use.commonSigma,id)
``` |

`d` |
This is a PLNseq object. |

`M` |
The number of simulations used in Monte-Carlo method for calculating likelihood ratio test statistics. |

`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 14 | ```
data(lung);
count = lung[,c(2:4,8:10)];
d = PLNobject(count,conditionNumber=2);
d = sizeFactor(d,maxCount=2e3);
## Not run:
## d = commonSigma(d);
## J = nrow(count);
## J1 = round(J/2);
## d$commonCorrelation = FALSE;
## d$cluster = c(rep(1,J1),rep(2,J-J1));
## d = correlationCoefficient(d);
## d = genewiseSigma(d);
## d = LRtest2(d,M=3e4,use.commonSigma=FALSE,id=1:100);
``` |

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