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Calculate Theoretical Scores for a Position-Specific Scoring Matrix (PSSM)

pssm_theoretical_max.Rd

These functions compute theoretical scores (maximum, minimum, and quantiles) that can be achieved by sequences matching a given Position-Specific Scoring Matrix (PSSM).

Usage

pssm_theoretical_max(pssm, prior = 0.01, regularization = 0.01)

pssm_theoretical_min(pssm, prior = 0.01, regularization = 0.01)

pssm_quantile(pssm, q, prior = 0.01, regularization = 0.01)

Arguments

pssm

A matrix or data frame containing position-specific probabilities for nucleotides A, C, G, T

prior

A numeric value (default: 0.01) added to each probability to avoid zero probabilities

regularization

A numeric value (default: 0.01) added inside the log function to prevent -Inf values

q

A numeric value between 0 and 1 specifying the quantile to calculate (only for pssm_quantile)

Value

  • pssm_theoretical_max: Maximum possible score for the given PSSM

  • pssm_theoretical_min: Minimum possible score for the given PSSM

  • pssm_quantile: Score at the specified quantile between min and max scores

Details

The functions normalize the probabilities and calculate scores based on logarithms with regularization. The quantile function interpolates linearly between min and max scores.

Examples

pssm <- as.matrix(MOTIF_DB["HOMER.CTCF"])
pssm_theoretical_max(pssm)
#> [1] -17.47226
pssm_theoretical_min(pssm)
#> [1] -123.9643
pssm_quantile(pssm, 0.85)
#> [1] -33.44606