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

This function computes the conditional probabilities *t_{ik}* that an observation *i* arises from the *kth* component for the current value of the mixture parameters.

1 |

`y` |
( |

`g` |
Number of clusters |

`conds` |
Vector of length |

`pi` |
Vector of length |

`s` |
Vector of length |

`lambda` |
( |

`t ` |
( |

If all values of *t_{ik}* are 0 (or nearly zero), the observation is assigned with probability one to belong to the cluster with the closest mean (in terms of the Euclidean distance from the observation). To avoid calculation difficulties, extreme values of *t_{ik}* are smoothed, such that those smaller than 1e-10 or larger than 1-1e-10 are set equal to 1e-10 and 1-1e-10, respectively.

Andrea Rau <[email protected]>

Rau, A., Maugis-Rabusseau, C., Martin-Magniette, M.-L., Celeux G. (2015). Co-expression analysis of high-throughput transcriptome sequencing data with Poisson mixture models. Bioinformatics, 31(9):1420-1427.

Rau, A., Celeux, G., Martin-Magniette, M.-L., Maugis-Rabusseau, C. (2011). Clustering high-throughput sequencing data with Poisson mixture models. Inria Research Report 7786. Available at http://hal.inria.fr/inria-00638082.

`PoisMixClus`

for Poisson mixture model estimation and model selection;
`PoisMixMean`

to calculate the conditional per-cluster mean of each observation

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 | ```
set.seed(12345)
## Simulate data as shown in Rau et al. (2011)
## Library size setting "A", high cluster separation
## n = 200 observations
simulate <- PoisMixSim(n = 200, libsize = "A", separation = "high")
y <- simulate$y
conds <- simulate$conditions
s <- colSums(y) / sum(y) ## TC estimate of lib size
## Run the PMM-II model for g = 3
## "TC" library size estimate, EM algorithm
run <- PoisMixClus(y, g = 3, norm = "TC",
conds = conds)
pi.est <- run$pi
lambda.est <- run$lambda
## Calculate the conditional probability of belonging to each cluster
proba <- probaPost(y, g = 3, conds = conds, pi = pi.est, s = s,
lambda = lambda.est)
## head(round(proba,2))
``` |

HTSCluster documentation built on May 29, 2017, 3:54 p.m.

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