# Identifying Protein Binding Sites in High-Throughput Sequencing Data

## Documentation for package ‘ChIPseqR’ version 1.40.0

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

## Help Pages

A B C D E G H L M N P R S T W misc

ChIPseqR-package | Identifying Protein Binding Sites in High-Throughput Sequencing Data

## -- A --

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

## -- B --

binding | Access slots of S4 classes
binding-method | Class "BindScore"
binding-method | Access slots of S4 classes
binding-methods | Access slots of S4 classes
BindScore | Class "BindScore"
BindScore-class | Class "BindScore"

## -- 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 --

exportBindSequence | 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 --

head-method | Class "BindScore"

## -- L --

lapply-method | Class "BindScore"
lapply-method | Class "ReadCounts"
length-method | Class "BindScore"
length-method | Class "ReadCounts"
length<--method | Class "BindScore"
length<--method | Class "ReadCounts"

## -- 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 --

tail-method | Class "BindScore"

## -- W --

windowCounts | Summarize read counts in a sliding window

## -- misc --

$-method | Class "ReadCounts"
$<--method | Class "ReadCounts"
[-method | Class "BindScore"
[-method | Class "ReadCounts"
[<--method | Class "ReadCounts"
[[-method | Class "BindScore"
[[-method | Class "ReadCounts"
[[<--method | Class "ReadCounts"