$-method | Names of variables |
$-method | Names of variables |
$-method | Names of variables |
$-method | Names of variables |
$-method | Names of variables |
$-method | Names of variables |
.inputParamMotifs | Normalizes the motifs input argument for multiple functions... |
.inputParamSequences | Normalize the sequences input argument... |
.inputPFMfromMatrixOrPWM | Check the frequency matrix input parameter for motifSimilarity... |
.normalize.bg.seq | check consistency of bg... |
.normargPfm | Input parameter normalization for PWMUnscaled... |
.normargPriorParams | Input parameter normalization function for PWMUnscaled... |
affinitySequenceSet | Calculate total affinity over a set of sequences... |
cloverPvalue1seq | Calculate the Clover P-value as described in the Clover paper... |
cloverScore | Calculate the Clover score using the recursive formula from Frith et al... |
colMedians | Calculate medians of columns... |
colSds | Calculate standard deviations of columns... |
concatenateSequences | Concatenata DNA sequences into a single character object... |
cutoffZscore | Z-score calculation for cutoff hits... |
cutoffZscoreSequenceSet | Z-score calculation for cutoff hits for group of sequences... |
divideRows | Divide each row of a matrix with a vector... |
DNAStringSetToList | Convert DNAStringSet to list of DNAString objects... |
empiricalPvalue | Calculate the empirical P-value by affinity of cutoff. |
empiricalPvalueSequenceSet | Empirical P-value for a set of sequences... |
getBackgroundFrequencies | Get the four nucleotides background frequencies... |
gevPerSequence | Apply GEV background normalization per every sequence... |
keepFinite | Replace all infinite values by 0... |
length | Names of variables |
length-method | Names of variables |
logNormPval | Calculate the P-value from lognormal distribution with background of equal length... |
logNormPvalSequenceSet | Lognormal P-value for a set of sequences... |
makeBackground | Make a background for a set of position frequency matrices... |
makePriors | Make priors from background sequences... |
makePWMCutoffBackground | Make a cutoff background... |
makePWMEmpiricalBackground | Make an empirical P-value background... |
makePWMGEVBackground | Make a GEV background distribution... |
makePWMLognBackground | Make a lognormal background distribution... |
makePWMPvalCutoffBackground | Construct a cutoff background from empirical background... |
makeStartEndPos | Divide total... |
matrixShuffleZscorePerSequence | Obtain z-score for motif column shuffling... |
maxAligned | Returned the aligned motif parts... |
motifDiffEnrichment | Differential motif enrichment |
motifEnrichment | Motif enrichment |
MotifEnrichmentResults | A wrapper class for results of motifEnrichment() that should make it easier to access the results. |
MotifEnrichmentResults-class | A wrapper class for results of motifEnrichment() that should make it easier to access the results. |
motifIC | Information content for a PWM or PFM... |
motifPrAUC | Calculate PR-AUC for motifs ranked according to some scoring scheme... |
motifRankingForGroup | Get a ranking of motifs by their enrichment in the whole set of sequences... |
motifRankingForGroup-method | Get a ranking of motifs by their enrichment in the whole set of sequences... |
motifRankingForSequence | Get a ranking of motifs by their enrichment in one specific sequence... |
motifRankingForSequence-method | Get a ranking of motifs by their enrichment in one specific sequence... |
motifRecoveryAUC | Calculate Recovery-AUC for motifs ranked according to some scoring scheme... |
motifScores | Motif affinity of number of hits over a threshold... |
motifScoresBigMemory | This is a memory intensive version of motifScore() which is abount 2 times faster... |
motifSimilarity | Calculates similarity between two PFMs. |
names-method | Names of variables |
names-method | Names of variables |
names-method | Names of variables |
names-method | Names of variables |
names-method | Names of variables |
names-method | Names of variables |
PFMtoPWM | Convert frequencies into motifs using PWMUnscaled... |
pickGenome | A helper function to pick a genome for an organism... |
plot | Plotting for the PWM class... |
plot-method | Plotting for the PWM class... |
plotMultipleMotifs | Plot mulitple motifs in a single plot... |
plotPFM | Plot a PFM (not PWM) using seqLogo... |
plotTopMotifsGroup | Plot the top N enrichment motifs in a group of sequences... |
plotTopMotifsGroup-method | Plot the top N enrichment motifs in a group of sequences... |
plotTopMotifsSequence | Plot the top N enrichment motifs in a single sequence... |
plotTopMotifsSequence-method | Plot the top N enrichment motifs in a single sequence... |
PWM | A class that represents a Position Weight Matrix (PWM)... |
PWM-class | A class that represents a Position Weight Matrix (PWM)... |
PWMCutoffBackground | Hit count background distribution for a set of PWMs... |
PWMCutoffBackground-class | Hit count background distribution for a set of PWMs... |
PWMEmpiricalBackground | Background for calculating empirical P-values... |
PWMEmpiricalBackground-class | Background for calculating empirical P-values... |
PWMGEVBackground | Generalized Extreme Values (GEV) background for P-values... |
PWMGEVBackground-class | Generalized Extreme Values (GEV) background for P-values... |
PWMLognBackground | Lognormal background distribution for a set of PWMs... |
PWMLognBackground-class | Lognormal background distribution for a set of PWMs... |
PWMUnscaled | Create a PWM from PFM |
rankingProcessAndReturn | A helper function for motifRankingForGroup and motifRankingForSequence with the common code... |
readJASPAR | Read motifs in JASPAR format... |
readMotifs | Read in motifs in JASPAR or TRANSFAC format... |
readTRANSFAC | Read in motifs in TRANSFAC format... |
registerCoresPWMEnrich | Register than PWMEnrich can use parallel CPU cores... |
reverseComplement | Reverse complement for the PWM object... |
reverseComplement-method | Reverse complement for the PWM object... |
scanWithPWM | Scan the whole sequence on both strands... |
seqLogoGrid | Draw a motif logo on an existing viewport... |
show-method | show method for MotifEnrichmentResults... |
show-method | show method for PWM... |
show-method | show method for PWMCutoffBackground... |
show-method | show method for PWMEmpiricalBackground... |
show-method | show method for PWMGEVBackground... |
show-method | show method for PWMLognBackground... |
tryAllMotifAlignments | Try all motif alignments and return max score... |
useBigMemoryPWMEnrich | If to use a faster implementation of motif scanning that requires abount 5 to 10 times more memory... |