# motifbreakR: an Introduction In motifbreakR: A Package For Predicting The Disruptiveness Of Single Nucleotide Polymorphisms On Transcription Factor Binding Sites

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## Calculate P-values for PWM match

Additionally, now, with the use of r CRANpkg("TFMPvalue"), we may filter by p-value of the match. This is unfortunately a two step process. First, by invoking filterp=TRUE and setting a threshold at a desired p-value e.g 1e-4, we perform a rough filter on the results by rounding all values in the PWM to two decimal place, and calculating a scoring threshold based upon that. The second step is to use the function calculatePvalue() on a selection of results which will change the Refpvalue and Altpvalue columns in the output from NA to the p-value calculated by TFMsc2pv. This can be (although not always) a very memory and time intensive process if the algorithm doesn't converge rapidly.

# Session Info

sessionInfo()


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motifbreakR documentation built on Nov. 8, 2020, 5:31 p.m.