R/RcppExports.R
em_count.RdCount transcripts using an Expectation Maximization (EM) algorithm.
em_count(txreads, txlengths, weights, ntx, nr, maxit = 1000L, reltol = 0.01, abstol = 0.01)
| txreads | A minimal matrix where each row corresponds to an alignment. The first column denotes transcript indices in [0, ntx-1] and the second column denotes read indices in [0, nr -1]. |
|---|---|
| txlengths | The sequence lengths for each transcript. Ideally those should be the effective transcript lengths meaning the overall number of possible alignment start positions in a transcript. |
| weights | Weights for individual alignments. |
| ntx | The total number of unique transcripts. |
| nr | The total number of unique reads. |
| maxit | Maximum number of EM iterations. |
| reltol | The relative tolerance for convergence. |
| abstol | The absolute tolerance for convergence. |
A list with the following components.
The length-normalized and read scaled transcript counts
The number of used EM iterations
The number of equivalence classes
The last osbserved absolute change in transcript counts