Description Usage Arguments Value Author(s) References Examples

Computes the P-value associated with a score threshold.

1 2 |

`mat` |
The input matrix. It can be a Position Frequency Matrix (PFM) or Position Weight Matrix (PWM) in log ratio. The matrix must have row names with "A", "C", "G", "T". |

`score` |
The required score. |

`bg` |
The background frequency of the sequences. A numeric vector with names "A", "C", "G", "T". |

`type` |
The type of input matrix. Can be "PFM" or "PWM". |

The P-value is returned based on the matrix, given the desired score.

Ge Tan

Touzet, H., and Varre, J.-S. (2007). Efficient and accurate P-value computation for Position Weight Matrices. Algorithms Mol Biol 2, 15.

1 2 3 4 5 6 7 8 9 10 | ```
pfm <- matrix(c(3, 5, 4, 2, 7, 0, 3, 4, 9, 1, 1, 3, 3, 6, 4, 1, 11,
0, 3, 0, 11, 0, 2, 1, 11, 0, 2, 1, 3, 3, 2, 6, 4, 1,
8, 1, 3, 4, 6, 1, 8, 5, 1, 0, 8, 1, 4, 1, 9, 0, 2, 3,
9, 5, 0, 0, 11, 0, 3, 0, 2, 7, 0, 5),
nrow = 4, dimnames = list(c("A","C","G","T"))
)
bg <- c(A=0.25, C=0.25, G=0.25, T=0.25)
score <- 8.77
type <- "PFM"
pvalue <- TFMsc2pv(pfm, score, bg, type)
``` |

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.