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

View source: R/associatePosteriors.R

This function aims to find pairwise dissimilarities between genes. It does this by comparing the posterior likelihoods of patterns of differential expression for each gene, and estimating the likelihood that the two genes are not equivalently expressed.

1 | ```
associatePosteriors(cD, maxsize = 250000, matrixFile = NULL)
``` |

`cD` |
A |

`maxsize` |
The maximum size (in MB) to use when partitioning the data. |

`matrixFile` |
If given, a file to write the complete (gzipped) matrix of pairwise distances between genes. Defaults to NULL. |

In comparing two genes, we find all patterns of expression considered
in the '@groups' slot of the 'cD' (`countData`

)
object for which the expression of the two genes can be considered
monotonic. We then subtract the sum the posterior likelihods of these
patterns of expression from 1 to define a likelihood of dissimilarity
between the two genes.

A data.frame which for each gene defines its nearest neighbour of higher row index and the dissimilarity with that neighbour.

Thomas J. Hardcastle

`makeClusters`

`makeClustersFF`

`kCluster`

1 2 3 4 5 6 | ```
# load in analysed countData (baySeq package) object
library(baySeq)
data(cD.ratThymus, package = "clusterSeq")
# estimate likelihoods of dissimilarity on reduced set
aM <- associatePosteriors(cD.ratThymus[1:1000,])
``` |

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