Man pages for cobindR
Finding Co-occuring motifs of transcription factor binding sites

bg_binding_sitesmotif hits in the background sequences
bg_pairsmotif hit pairs in the background sequences
bg_sequence_originbackground sequence origin note
bg_sequenceslist of background sequence
bg_sequence_sourcebackground sequence source note
bg_sequence_typebackground sequence type note
binding_sitesmotif hits on the foreground sequences
cobindr-classClass '"cobindr"'
cobindRConfigurationcobindR configuration object constructor
cobindr-internalInternal cobindr Functions
cobindr-packageAn R package for analyzing co-occurring transcription factor...
commentcomment of cobindR SeqObj object
configurationconfiguration of cobindr object
configuration-classClass '"configuration"'
downstreamdownstream range [bp] used in experiment
experiment_descriptiondescription of cobindR or configuration object
fdrThresholdfdrThreshold of cobindR configuration object
find.pairsfunction to find pairs of binding sites for every sequence in...
get.bindingsite.rangesconvenience function to convert predicted binding sites to...
get.pairsfunction to get output of findPairs
get.significant.pairsfunction to returns the results of detrending as a data.frame
idid of cobindR configuration object
locationlocation of cobindR SeqObj object
martbiomart of cobindR configuration object
max_distancemax_distance of cobindR configuration object
namename of cobindR SeqObj object
pairsmotif hit pairs in the foreground sequences
pairs_of_interestpairs_of_interest of cobindr object
pathpath of cobindR configuration object
pfmpfm list used in experiment
pfm_pathpath to pfms to be used
plot.detrendingfunction to plot distances between a pair of PWMs
plot.gcfunction to visualize GC content or CpG content of input...
plot.pairdistancefunction to plot the distance of the pairs in the sequences
plot.pairdistributionfunction to plot the distribution of the number of pairs in...
plot.positionprofilefunction to plot a profile over the total number of predicted...
plot.positionsfunction to plot hits for each PWM on the individual sequence
plot.positions.simplefunction to plot hits for each PWM on the individual sequence
plot.tfbs.heatmapfunction to do plot a heatmap of overlaps between all...
plot.tfbslogofunction to plot sequence logos based on hits of tools
plot.tfbs.venndiagramfunction visualize the overlaps of PWM hits over the...
predicted2pwmfunction to convert predicted TFBS hits into a PWM
pseudocountpseudocount of cobindR configuration object
pValuepValue threshold used for motif hit finding
rtfbsfunction performs TFBS prediction using the package rtfbs
search.gademfunction performs TFBS prediction denovo or based on transfac...
search.pwmfunction to predict transcription factor binding sites using...
seqObjcobindR SeqObj object constructor
SeqObj-classClass '"SeqObj"'
sequencereturns sequence of cobindR SeqObj object
sequence_originreturns sequence_origin of cobindR configuration object
sequencessequences of cobindr object
sequence_sourcereturns sequence_source of cobindR configuration object
sequence_typesequence type of cobindR configuration object
speciesspecies of cobindR configuration or SeqObj
testCpGfunction to cluster sequences based on their CpG and GC...
thresholdthreshold used in motif hit finding
uiduid of cobindR SeqObj object
upstreamupstream range [bp] used in experiment
write.bindingsiteswrites predicted binding sites as a BED file.
write.bindingsites.tablefunction to write predicted TFBS into a tab-separated file.
write.pairsfunction to write output of findPairs into file
write.sequenceswrites the sequences of a cobindr-object into a fasta file.
cobindR documentation built on April 28, 2020, 6:40 p.m.