Identifying Protein Binding Sites in High-Throughput Sequencing Data

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Documentation for package ‘ChIPseqR’ version 1.42.0

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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"