Finding Co-occuring motifs of transcription factor binding sites


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Documentation for package ‘cobindR’ version 1.4.0

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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.