A C D E G K L M N P R S T U misc
affinitySequenceSet | Calculate total affinity over a set of sequences |
as.data.frame | Convert a MotifEnrichmentReport into a data.frame object |
as.data.frame-method | Convert a MotifEnrichmentReport into a data.frame object |
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 |
getPromoters | Get the promoter sequences either for a named organism such as "dm3" or a BSgenome object |
gevPerSequence | Apply GEV background normalization per every sequence |
groupReport | Generate a motif enrichment report for the whole group of sequences together |
groupReport-method | Generate a motif enrichment report for the whole group of sequences together |
keepFinite | Replace all infinite values by 0 |
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 |
makePWMPvalCutoffBackgroundFromSeq | Construct a P-value cutoff background from a set of sequences |
makeStartEndPos | Divide total.len into fragments of length len by providing start,end positions |
matrixShuffleZscorePerSequence | Obtain z-score for motif column shuffling |
maxAligned | Returned the aligned motif parts |
motifDiffEnrichment | Differential motif enrichment |
motifEcdf | Calculate the empirical distribution score distribution for a set of motifs |
motifEnrichment | Motif enrichment |
MotifEnrichmentReport-class | A report class with formatted results of motif enrichment |
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 or number of hits over a threshold |
motifScoresBigMemory | This is a memory intensive version of motifScore() which is about 2 times faster |
motifSimilarity | Calculates similarity between two PFMs. |
names,MotifEnrichmentReport | Names of variables |
names,MotifEnrichmentResults | Names of variables |
names,PWM | Names of variables |
names,PWMCutoffBackground | Names of variables |
names,PWMEmpiricalBackground | Names of variables |
names,PWMGEVBackground | Names of variables |
names,PWMLognBackground | 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 |
names-method | Names of variables |
names-method | Names of variables |
PFMtoPWM | Convert frequencies into motifs using PWMUnscaled |
plot-method | Plot the motif enrichment report |
plot-method | Plotting for the PWM class |
plotMotifScores | Plot the raw motifs scores as returned by motifScores() |
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-class | A class that represents a Position Weight Matrix (PWM) |
PWMCutoffBackground-class | Hit count background distribution for a set of PWMs |
PWMEmpiricalBackground-class | Background for calculating empirical P-values |
PWMGEVBackground-class | Generalized Extreme Values (GEV) background for P-values |
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-method | Reverse complement for the PWM object |
scanWithPWM | Scan the whole sequence on both strands |
seqLogoGrid | Draw a motif logo on an existing viewport |
sequenceReport | Generate a motif enrichment report for a single sequence |
sequenceReport-method | Generate a motif enrichment report for a single sequence |
show-method | show method for MotifEnrichmentReport |
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 |
toPWM | Convert motifs into PWMs |
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 |
$-method | Names of variables |
$-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.seq input parameter |
.normargPfm | Input parameter normalization for PWMUnscaled |
.normargPriorParams | Input parameter normalization function for PWMUnscaled |
[-method | Names of variables |
[-method | Get the background for a subset of PWMs |
[-method | Get the background for a subset of PWMs |
[-method | Get the background for a subset of PWMs |
[-method | Get the background for a subset of PWMs |