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cobindR (version 1.10.0)

Finding Co-occuring motifs of transcription factor binding sites

Description

Finding and analysing co-occuring motifs of transcription factor binding sites in groups of genes

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Version

Version

1.10.0

License

Artistic-2.0

Maintainer

Manuela Benary

Last Published

February 15th, 2017

Functions in cobindR (1.10.0)

cobindr-internal

Internal cobindr Functions
pairs_of_interest

pairs_of_interest of cobindr object
get.significant.pairs

function to returns the results of detrending as a data.frame
plot.pairdistribution

function to plot the distribution of the number of pairs in the sequences
cobindr-class

Class "cobindr"
configuration-class

Class "configuration"
get.pairs

function to get output of findPairs
cobindR-package

An R package for analyzing co-occurring transcription factor binding sites
find.pairs

function to find pairs of binding sites for every sequence in a given object of class "cobindr"
predicted2pwm

function to convert predicted TFBS hits into a PWM
rtfbs

function performs TFBS prediction using the package rtfbs
bg_sequence_source

background sequence source note
bg_binding_sites

motif hits in the background sequences
bg_sequences

list of background sequence
bg_sequence_type

background sequence type note
bg_pairs

motif hit pairs in the background sequences
configuration

configuration of cobindr object
experiment_description

description of cobindR or configuration object
binding_sites

motif hits on the foreground sequences
downstream

downstream range [bp] used in experiment
pfm_path

path to pfms to be used
pValue

pValue threshold used for motif hit finding
pairs

motif hit pairs in the foreground sequences
comment

comment of cobindR SeqObj object
cobindRConfiguration

cobindR configuration object constructor
path

path of cobindR configuration object
fdrThreshold

fdrThreshold of cobindR configuration object
plot.tfbs.heatmap

function to do plot a heatmap of overlaps between all specified PWMs
pfm

pfm list used in experiment
seqObj

cobindR SeqObj object constructor
sequence_source

returns sequence_source of cobindR configuration object
write.bindingsites

writes predicted binding sites as a BED file.
plot.positions

function to plot hits for each PWM on the individual sequence
plot.tfbslogo

function to plot sequence logos based on hits of tools
location

location of cobindR SeqObj object
name

name of cobindR SeqObj object
plot.detrending

function to plot distances between a pair of PWMs
plot.tfbs.venndiagram

function visualize the overlaps of PWM hits over the sequences.
sequences

sequences of cobindr object
threshold

threshold used in motif hit finding
sequence_origin

returns sequence_origin of cobindR configuration object
species

species of cobindR configuration or SeqObj
testCpG

function to cluster sequences based on their CpG and GC content
upstream

upstream range [bp] used in experiment
id

id of cobindR configuration object
max_distance

max_distance of cobindR configuration object
plot.pairdistance

function to plot the distance of the pairs in the sequences
plot.positionprofile

function to plot a profile over the total number of predicted transcription factor binding sites for each PWM.
uid

uid of cobindR SeqObj object
write.pairs

function to write output of findPairs into file
pseudocount

pseudocount of cobindR configuration object
sequence

returns sequence of cobindR SeqObj object
write.sequences

writes the sequences of a cobindr-object into a fasta file.
SeqObj-class

Class "SeqObj"
search.pwm

function to predict transcription factor binding sites using the method matchPWM from package Biostrings
search.gadem

function performs TFBS prediction denovo or based on transfac / jaspar matrices pwms using rGADEM.
plot.positions.simple

function to plot hits for each PWM on the individual sequence
bg_sequence_origin

background sequence origin note
mart

biomart of cobindR configuration object
get.bindingsite.ranges

convenience function to convert predicted binding sites to GRanges object.
sequence_type

sequence type of cobindR configuration object
write.bindingsites.table

function to write predicted TFBS into a tab-separated file.
plot.gc

function to visualize GC content or CpG content of input sequences