Identifying Protein Binding Sites in High-Throughput Sequencing Data

Documentation for package ‘ChIPseqR’ version 1.63.0

Help Pages

Identifying Protein Binding Sites in High-Throughput Sequencing Data

-- A --

alignFeature	Read counts relative to annotated features
as.data.frame-method	Class "BindScore"

-- B --

-- C --

callBindingSites	Predict protein binding sites from high-throughput sequencing data
callBindingSites-method	Predict protein binding sites from high-throughput sequencing data
callBindingSites-methods	Predict protein binding sites from high-throughput sequencing data
ChIPseqR	Identifying Protein Binding Sites in High-Throughput Sequencing Data
chrLength	Class "ReadCounts"
chrLength-method	Class "BindScore"
chrLength-method	Run-length Encoded Read Counts
chrLength-method	Class "ReadCounts"
compress	Methods for Function compress in Package 'ChIPseqR'
compress-BindScore	Compress BindScore Objects
compress-method	Compress BindScore Objects
compress-method	Compress ReadCount Objects
compress-method	Methods for Function compress in Package 'ChIPseqR'
compress-methods	Methods for Function compress in Package 'ChIPseqR'
cutoff	Access slots of S4 classes
cutoff-method	Class "BindScore"
cutoff-method	Access slots of S4 classes
cutoff-methods	Access slots of S4 classes
cutoff<-	Access slots of S4 classes
cutoff<--method	Class "BindScore"
cutoff<--method	Access slots of S4 classes
cutoff<--methods	Access slots of S4 classes

-- D --

decompress	Extract Read Count and Binding Site Score Representations
decompress-method	Methods for Function decompress in Package 'ChIPseqR'
decompress-method	Extract Read Count and Binding Site Score Representations
decompress-methods	Methods for Function decompress in Package 'ChIPseqR'

-- E --

Export sequence of predicted binding sites

-- G --

getBindCor	Calculate cross-correlation between read counts
getBindLen	Estimate length of binding and support region
getCutoff	Determine significance threshold for binding site scores

-- H --

Class "BindScore"

-- L --

-- M --

max-method	Class "BindScore"
min-method	Class "BindScore"

-- N --

names-method	Class "BindScore"
names-method	Class "ReadCounts"
names<--method	Class "BindScore"
names<--method	Class "ReadCounts"
nreads	Class "ReadCounts"
nreads-method	Run-length Encoded Read Counts
nreads-method	Class "ReadCounts"
nullDist	Access slots of S4 classes
nullDist-method	Class "BindScore"
nullDist-method	Access slots of S4 classes
nullDist-methods	Access slots of S4 classes
nullDist<-	Access slots of S4 classes
nullDist<--method	Class "BindScore"
nullDist<--method	Access slots of S4 classes
nullDist<--methods	Access slots of S4 classes

-- P --

peaks	Access slots of S4 classes
peaks-method	Class "BindScore"
peaks-method	Access slots of S4 classes
peaks-methods	Access slots of S4 classes
pickPeak	Identify peaks above a given threshold
plot-method	Diagnostic Plots for Binding Site Scores
plot-method	Diagnostic Plots for Read Counts
pos2gff	Convert genome coordinates into GFF format
pvalue	Access slots of S4 classes
pvalue-method	Access slots of S4 classes
pvalue-methods	Access slots of S4 classes

-- R --

range-method	Class "BindScore"
ReadCounts	Class "ReadCounts"
ReadCounts-class	Class "ReadCounts"
RLEBindScore-class	Run-length Encoded Binding Site Scores
RLEReadCounts-class	Run-length Encoded Read Counts

-- S --

sapply-method	Class "ReadCounts"
score	Access slots of S4 classes
score-method	Class "BindScore"
simpleNucCall	Predict nucleosome positions from high-throughput sequencing data
startScore	Score potential protein binding sites
strandPileup	Strand specific read counts
strandPileup-method	Strand specific read counts
strandPileup-methods	Strand specific read counts
support	Access slots of S4 classes
support-method	Class "BindScore"
support-method	Access slots of S4 classes
support-methods	Access slots of S4 classes

-- T --

Class "BindScore"

-- W --

Summarize read counts in a sliding window

-- misc --