# Finding Co-occuring motifs of transcription factor binding sites

## Documentation for package ‘cobindR’ version 1.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

B C D E F G I L M N P R S T U W

cobindR-package | An R package for analyzing co-occurring transcription factor binding sites
cobindr-package | An R package for analyzing co-occurring transcription factor binding sites

## -- B --

bg_binding_sites | motif hits in the background sequences
bg_binding_sites-method | motif hits in the background sequences
bg_binding_sites<- | motif hits in the background sequences
bg_binding_sites<--method | motif hits in the background sequences
bg_pairs | motif hit pairs in the background sequences
bg_pairs-method | motif hit pairs in the background sequences
bg_pairs<- | motif hit pairs in the background sequences
bg_pairs<--method | motif hit pairs in the background sequences
bg_sequences | list of background sequence
bg_sequences-method | list of background sequence
bg_sequences<- | list of background sequence
bg_sequences<--method | list of background sequence
bg_sequence_origin | background sequence origin note
bg_sequence_origin-method | background sequence origin note
bg_sequence_origin<- | background sequence origin note
bg_sequence_origin<--method | background sequence origin note
bg_sequence_source | background sequence source note
bg_sequence_source-method | background sequence source note
bg_sequence_source<- | background sequence source note
bg_sequence_source<--method | background sequence source note
bg_sequence_type | background sequence type note
bg_sequence_type-method | background sequence type note
bg_sequence_type<- | background sequence type note
bg_sequence_type<--method | background sequence type note
binding_sites | motif hits on the foreground sequences
binding_sites-method | motif hits on the foreground sequences
binding_sites<- | motif hits on the foreground sequences
binding_sites<--method | motif hits on the foreground sequences

## -- C --

cobindR | An R package for analyzing co-occurring transcription factor binding sites
cobindr | An R package for analyzing co-occurring transcription factor binding sites
cobindr-class | Class '"cobindr"'
cobindRConfiguration | cobindR configuration object constructor
cobindRConfiguration-method | cobindR configuration object constructor
comment | comment of cobindR SeqObj object
comment-method | comment of cobindR SeqObj object
comment<- | comment of cobindR SeqObj object
comment<--method | comment of cobindR SeqObj object
configuration | configuration of cobindr object
configuration-class | Class '"configuration"'
configuration-method | configuration of cobindr object
configuration<- | configuration of cobindr object
configuration<--method | configuration of cobindr object

## -- D --

detrending-method | Class '"cobindr"'
downstream | downstream range [bp] used in experiment
downstream-method | downstream range [bp] used in experiment
downstream<- | downstream range [bp] used in experiment
downstream<--method | downstream range [bp] used in experiment

## -- E --

experiment_description | description of cobindR or configuration object
experiment_description-method | description of cobindR or configuration object
experiment_description<- | description of cobindR or configuration object
experiment_description<--method | description of cobindR or configuration object

## -- F --

fdrThreshold | fdrThreshold of cobindR configuration object
fdrThreshold-method | fdrThreshold of cobindR configuration object
fdrThreshold<- | fdrThreshold of cobindR configuration object
fdrThreshold<--method | fdrThreshold of cobindR configuration object
find.pairs | function to find pairs of binding sites for every sequence in a given object of class "cobindr"
find.pairs-method | Class '"cobindr"'

## -- G --

generate.background-method | Class '"cobindr"'
get.bindingsite.ranges | convenience function to convert predicted binding sites to GRanges object.
get.bindingsite.ranges-method | Class '"cobindr"'
get.pairs | function to get output of findPairs
get.pairs-method | function to get output of findPairs
get.significant.pairs | function to returns the results of detrending as a data.frame
get.significant.pairs-method | function to returns the results of detrending as a data.frame

## -- I --

id | id of cobindR configuration object
id-method | id of cobindR configuration object
id<- | id of cobindR configuration object
id<--method | id of cobindR configuration object
initialize-method | Class '"SeqObj"'
initialize-method | Class '"cobindr"'
initialize-method | Class '"configuration"'
input.pwm-method | Class '"cobindr"'

## -- L --

location | location of cobindR SeqObj object
location-method | location of cobindR SeqObj object
location<- | location of cobindR SeqObj object
location<--method | location of cobindR SeqObj object

## -- M --

mart | biomart of cobindR configuration object
mart-method | biomart of cobindR configuration object
mart<- | biomart of cobindR configuration object
mart<--method | biomart of cobindR configuration object
max_distance | max_distance of cobindR configuration object
max_distance-method | max_distance of cobindR configuration object
max_distance<- | max_distance of cobindR configuration object
max_distance<--method | max_distance of cobindR configuration object

## -- N --

name | name of cobindR SeqObj object
name-method | name of cobindR SeqObj object
name<- | name of cobindR SeqObj object
name<--method | name of cobindR SeqObj object

## -- P --

pairs | motif hit pairs in the foreground sequences
pairs-method | motif hit pairs in the foreground sequences
pairs<- | motif hit pairs in the foreground sequences
pairs<--method | motif hit pairs in the foreground sequences
pairs_of_interest | pairs_of_interest of cobindr object
pairs_of_interest-method | pairs_of_interest of cobindr object
pairs_of_interest<- | pairs_of_interest of cobindr object
pairs_of_interest<--method | pairs_of_interest of cobindr object
path | path of cobindR configuration object
path-method | path of cobindR configuration object
path<- | path of cobindR configuration object
path<--method | path of cobindR configuration object
pfm | pfm list used in experiment
pfm-method | pfm list used in experiment
pfm<- | pfm list used in experiment
pfm<--method | pfm list used in experiment
pfm_path | path to pfms to be used
pfm_path-method | path to pfms to be used
pfm_path<- | path to pfms to be used
pfm_path<--method | path to pfms to be used
plot.detrending | function to plot distances between a pair of PWMs
plot.detrending-method | function to plot distances between a pair of PWMs
plot.gc | function to visualize GC content or CpG content of input sequences
plot.gc-method | function to visualize GC content or CpG content of input sequences
plot.pairdistance | function to plot the distance of the pairs in the sequences
plot.pairdistance-method | function to plot the distance of the pairs in the sequences
plot.pairdistribution | function to plot the distribution of the number of pairs in the sequences
plot.pairdistribution-method | function to plot the distribution of the number of pairs in the sequences
plot.positionprofile | function to plot a profile over the total number of predicted transcription factor binding sites for each PWM.
plot.positionprofile-method | function to plot a profile over the total number of predicted transcription factor binding sites for each PWM.
plot.positions | function to plot hits for each PWM on the individual sequence
plot.positions-method | 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.positions.simple-method | function to plot hits for each PWM on the individual sequence
plot.tfbs.heatmap | function to do plot a heatmap of overlaps between all specified PWMs
plot.tfbs.heatmap-method | function to do plot a heatmap of overlaps between all specified PWMs
plot.tfbs.venndiagram | function visualize the overlaps of PWM hits over the sequences.
plot.tfbs.venndiagram-method | function visualize the overlaps of PWM hits over the sequences.
plot.tfbslogo | function to plot sequence logos based on hits of tools
plot.tfbslogo-method | function to plot sequence logos based on hits of tools
predicted2pwm | function to convert predicted TFBS hits into a PWM
predicted2pwm-method | function to convert predicted TFBS hits into a PWM
pseudocount | pseudocount of cobindR configuration object
pseudocount-method | pseudocount of cobindR configuration object
pseudocount<- | pseudocount of cobindR configuration object
pseudocount<--method | pseudocount of cobindR configuration object
pValue | pValue threshold used for motif hit finding
pValue-method | pValue threshold used for motif hit finding
pValue<- | pValue threshold used for motif hit finding
pValue<--method | pValue threshold used for motif hit finding

## -- R --

read.background.fasta-method | Class '"configuration"'
read.pfm-method | Class '"configuration"'
read.sequences-method | Class '"configuration"'
rtfbs | function performs TFBS prediction using the package rtfbs
rtfbs-method | function performs TFBS prediction using the package rtfbs
rtfbs.intern-method | Class '"SeqObj"'

## -- S --

search.gadem | function performs TFBS prediction denovo or based on transfac / jaspar matrices pwms using rGADEM.
search.gadem-method | function performs TFBS prediction denovo or based on transfac / jaspar matrices pwms using rGADEM.
search.pwm | function to predict transcription factor binding sites using the method matchPWM from package Biostrings
search.pwm-method | function to predict transcription factor binding sites using the method matchPWM from package Biostrings
seqObj | cobindR SeqObj object constructor
SeqObj-class | Class '"SeqObj"'
seqObj-method | cobindR SeqObj object constructor
sequence | returns sequence of cobindR SeqObj object
sequence-method | returns sequence of cobindR SeqObj object
sequence<- | returns sequence of cobindR SeqObj object
sequence<--method | returns sequence of cobindR SeqObj object
sequences | sequences of cobindr object
sequences-method | sequences of cobindr object
sequences<- | sequences of cobindr object
sequences<--method | sequences of cobindr object
sequence_origin | returns sequence_origin of cobindR configuration object
sequence_origin-method | returns sequence_origin of cobindR configuration object
sequence_origin<- | returns sequence_origin of cobindR configuration object
sequence_origin<--method | returns sequence_origin of cobindR configuration object
sequence_source | returns sequence_source of cobindR configuration object
sequence_source-method | returns sequence_source of cobindR configuration object
sequence_source<- | returns sequence_source of cobindR configuration object
sequence_source<--method | returns sequence_source of cobindR configuration object
sequence_type | sequence type of cobindR configuration object
sequence_type-method | sequence type of cobindR configuration object
sequence_type<- | sequence type of cobindR configuration object
sequence_type<--method | sequence type of cobindR configuration object
species | species of cobindR configuration or SeqObj
species-method | species of cobindR configuration or SeqObj
species<- | species of cobindR configuration or SeqObj
species<--method | species of cobindR configuration or SeqObj

## -- T --

testCpG | function to cluster sequences based on their CpG and GC content
testCpG-method | function to cluster sequences based on their CpG and GC content
threshold | threshold used in motif hit finding
threshold-method | threshold used in motif hit finding
threshold<- | threshold used in motif hit finding
threshold<--method | threshold used in motif hit finding

## -- U --

uid | uid of cobindR SeqObj object
uid-method | uid of cobindR SeqObj object
uid<- | uid of cobindR SeqObj object
uid<--method | uid of cobindR SeqObj object
upstream | upstream range [bp] used in experiment
upstream-method | upstream range [bp] used in experiment
upstream<- | upstream range [bp] used in experiment
upstream<--method | upstream range [bp] used in experiment

## -- W --

write-method | Class '"cobindr"'
write-method | Class '"configuration"'
write.bindingsites | writes predicted binding sites as a BED file.
write.bindingsites-method | writes predicted binding sites as a BED file.
write.bindingsites.table | function to write predicted TFBS into a tab-separated file.
write.bindingsites.table-method | function to write predicted TFBS into a tab-separated file.
write.fasta-method | Class '"SeqObj"'
write.pairs | function to write output of findPairs into file
write.pairs-method | function to write output of findPairs into file
write.sequences | writes the sequences of a cobindr-object into a fasta file.
write.sequences-method | writes the sequences of a cobindr-object into a fasta file.