Man pages for matthuska/tRap
A biophysical model for transcription factor binding affinities

affinitycompute transcription factor binding site affinity
evaluate.rankingEvaluate Ranking
exactgevparamsPrecalculated generalized extreme value distribution...
fit.gevFit a gev distribution for a pwm matrix.
get.affinity.cutoffdetermine significance threshold for tRap affinities
gevparamsparameters for the fitted extreme value distributions for...
jasparThe JASPAR transcription factor database in the format...
local.paffinityCalculate local p-values
normalize.pwmnormalize a PWM
paffinitycompute p-values for affinity values
R_affinity_multiCalculate the TRAP affinity for each position along one or...
R_affinity_sum_multiCalculate the TRAP affinity for one or more sequences (one...
rank.factorsRank transcription factors according to changes in binding...
read.jasparread a jaspar matrix
read.pscmread a PSCM
read.transfacread a transfac matrix
read.transfac.dirread a directory of transfac matrices
scan.sequenceidentify TFBS hits in the sequence(s)
tRap-packagecompute transcription factor binding site affinity
matthuska/tRap documentation built on Nov. 9, 2017, 3:13 p.m.