Description Usage Arguments Value Author(s) Examples

View source: R/diffSeqLogoSupport.R

Enriches a matrix of difflogo objects with p-values which quantifies the probability that two PWM-positions are from the same distribution

1 2 | ```
enrichDiffLogoTableWithPvalues(diffLogoObjMatrix, sampleSizes,
stackHeight = shannonDivergence, numberOfPermutations = 100)
``` |

`diffLogoObjMatrix` |
matrix of difflogo objects |

`sampleSizes` |
number of sequences behind the pwms behind the given difflogo objects |

`stackHeight` |
function for the calculation of a divergence measure for two probability vectors |

`numberOfPermutations` |
the number of permutations to perform for the calculation of stackHeights |

matrix of difflogo objects enriched with p-values

Martin Nettling

1 2 3 4 5 6 7 8 9 10 11 12 13 | ```
motif_folder= "extdata/pwm"
motif_names = c("HepG2","MCF7","HUVEC","ProgFib")
motifs = list()
for (name in motif_names) {
fileName = paste(motif_folder,"/",name,".pwm",sep="")
file = system.file(fileName, package = "DiffLogo")
motifs[[name]] = getPwmFromPwmFile(file)
}
sampleSizes <- c(100, 150, 200, 250)
names(sampleSizes) <- motif_names
diffLogoTableObj = prepareDiffLogoTable(motifs);
diffLogoTableObj$diffLogoObjMatrix = enrichDiffLogoTableWithPvalues(diffLogoTableObj$diffLogoObjMatrix, sampleSizes)
``` |

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