PWMSimilarity-methods: PWMSimilarity method

In ge11232002/TFBSTools: Software Package for Transcription Factor Binding Site (TFBS) Analysis

PWMSimilarity method

Description

This function measures the similarity of two PWM matrix in three measurements: "normalised Euclidean distance", "Pearson correlation" and "Kullback Leibler divergence".

Usage

  PWMSimilarity(pwmSubject, pwmQuery, method=c("Euclidean", "Pearson", "KL"))

Arguments

pwmSubject	A matrix or PWMatrix or PWMatrixList object in “prob” type.
pwmQuery	A matrix or PWMatrix object.
method	The method can be "Euclidean", "Pearson", "KL".

Details

When pwmSubject and pwmQuery have different number of columns, the smaller PWM will be shifted from the start position of larger PWM and compare all the possible alignments. Only the smallest distance, divergence or largest correlation will be reported.

Value

A numeric value is returned.

Methods

signature(pwmSubject = "matrix", pwmQuery = "matrix")

signature(pwmSubject = "matrix", pwmQuery = "PWMatrix")

signature(pwmSubject = "PWMatrix", pwmQuery = "matrix")

signature(pwmSubject = "PWMatrix", pwmQuery = "PWMatrix")

signature(pwmSubject = "PWMatrixList", pwmQuery = "matrix")

signature(pwmSubject = "PWMatrixList", pwmQuery = "PWMatrix")

signature(pwmSubject = "PWMatrixList", pwmQuery = "PWMatrixList")

References

Linhart, C., Halperin, Y., & Shamir, R. (2008). Transcription factor and microRNA motif discovery: The Amadeus platform and a compendium of metazoan target sets. Genome Research, 18(7), 1180-1189. doi:10.1101/gr.076117.108

See Also

PFMSimilarity

Examples

  data(MA0003.2)
  data(MA0004.1)
  pwm1 = toPWM(MA0003.2, type="prob")
  pwm2 = toPWM(MA0004.1, type="prob")
  PWMSimilarity(pwm1, pwm2, method="Euclidean")

ge11232002/TFBSTools documentation built on Dec. 26, 2024, 12:38 a.m.