Man pages for cobindR
Finding Co-occuring motifs of transcription factor binding sites
| bg_binding_sites | motif hits in the background sequences |
| bg_pairs | motif hit pairs in the background sequences |
| bg_sequence_origin | background sequence origin note |
| bg_sequences | list of background sequence |
| bg_sequence_source | background sequence source note |
| bg_sequence_type | background sequence type note |
| binding_sites | motif hits on the foreground sequences |
| cobindr-class | Class '"cobindr"' |
| cobindRConfiguration | cobindR configuration object constructor |
| cobindr-internal | Internal cobindr Functions |
| cobindr-package | An R package for analyzing co-occurring transcription factor... |
| comment | comment of cobindR SeqObj object |
| configuration | configuration of cobindr object |
| configuration-class | Class '"configuration"' |
| downstream | downstream range [bp] used in experiment |
| experiment_description | description of cobindR or configuration object |
| fdrThreshold | fdrThreshold of cobindR configuration object |
| find.pairs | function to find pairs of binding sites for every sequence in... |
| get.bindingsite.ranges | convenience function to convert predicted binding sites to... |
| get.pairs | function to get output of findPairs |
| get.significant.pairs | function to returns the results of detrending as a data.frame |
| id | id of cobindR configuration object |
| location | location of cobindR SeqObj object |
| mart | biomart of cobindR configuration object |
| max_distance | max_distance of cobindR configuration object |
| name | name of cobindR SeqObj object |
| pairs | motif hit pairs in the foreground sequences |
| pairs_of_interest | pairs_of_interest of cobindr object |
| path | path of cobindR configuration object |
| pfm | pfm list used in experiment |
| pfm_path | path to pfms to be used |
| plot.detrending | function to plot distances between a pair of PWMs |
| plot.gc | function to visualize GC content or CpG content of input... |
| plot.pairdistance | function to plot the distance of the pairs in the sequences |
| plot.pairdistribution | function to plot the distribution of the number of pairs in... |
| plot.positionprofile | function to plot a profile over the total number of predicted... |
| plot.positions | function to plot hits for each PWM on the individual sequence |
| plot.positions.simple | function to plot hits for each PWM on the individual sequence |
| plot.tfbs.heatmap | function to do plot a heatmap of overlaps between all... |
| plot.tfbslogo | function to plot sequence logos based on hits of tools |
| plot.tfbs.venndiagram | function visualize the overlaps of PWM hits over the... |
| predicted2pwm | function to convert predicted TFBS hits into a PWM |
| pseudocount | pseudocount of cobindR configuration object |
| pValue | pValue threshold used for motif hit finding |
| rtfbs | function performs TFBS prediction using the package rtfbs |
| search.gadem | function performs TFBS prediction denovo or based on transfac... |
| search.pwm | function to predict transcription factor binding sites using... |
| seqObj | cobindR SeqObj object constructor |
| SeqObj-class | Class '"SeqObj"' |
| sequence | returns sequence of cobindR SeqObj object |
| sequence_origin | returns sequence_origin of cobindR configuration object |
| sequences | sequences of cobindr object |
| sequence_source | returns sequence_source of cobindR configuration object |
| sequence_type | sequence type of cobindR configuration object |
| species | species of cobindR configuration or SeqObj |
| testCpG | function to cluster sequences based on their CpG and GC... |
| threshold | threshold used in motif hit finding |
| uid | uid of cobindR SeqObj object |
| upstream | upstream range [bp] used in experiment |
| write.bindingsites | writes predicted binding sites as a BED file. |
| write.bindingsites.table | function to write predicted TFBS into a tab-separated file. |
| write.pairs | function to write output of findPairs into file |
| write.sequences | writes the sequences of a cobindr-object into a fasta file. |
