Identifying Protein Binding Sites in High-Throughput Sequencing Data


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Documentation for package ‘ChIPseqR’ version 1.0.0

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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

-- --

$,ReadCounts,ANY-method Class "ReadCounts"
$<-,ReadCounts,ANY,ANY-method Class "ReadCounts"
$<-,ReadCounts-method Class "ReadCounts"

-- A --

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

-- B --

binding Access slots of S4 classes
binding,ANY-method Access slots of S4 classes
binding,BindScore-method Class "BindScore"
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,ANY-method Predict protein binding sites from high-throughput sequencing data
callBindingSites,character-method Predict protein binding sites from high-throughput sequencing data
callBindingSites,matrix-method Predict protein binding sites from high-throughput sequencing data
callBindingSites,ReadCounts-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,BindScore-method Class "BindScore"
chrLength,ReadCounts-method Class "ReadCounts"
chrLength,RLEReadCounts-method Run-length Encoded Read Counts
compress Methods for Function compress in Package 'ChIPseqR'
compress,BindScore-method Compress BindScore Objects
compress,ReadCounts-method Compress ReadCount Objects
compress,RLEBindScore-method Methods for Function compress in Package 'ChIPseqR'
compress,RLEReadCounts-method Methods for Function compress in Package 'ChIPseqR'
compress-BindScore Compress BindScore Objects
compress-methods Methods for Function compress in Package 'ChIPseqR'
cutoff Access slots of S4 classes
cutoff,ANY-method Access slots of S4 classes
cutoff,BindScore-method Class "BindScore"
cutoff-methods Access slots of S4 classes
cutoff<- Access slots of S4 classes
cutoff<-,ANY-method Access slots of S4 classes
cutoff<-,BindScore-method Class "BindScore"
cutoff<--methods Access slots of S4 classes

-- D --

decompress Extract Read Count and Binding Site Score Representations
decompress,ANY-method Methods for Function decompress in Package 'ChIPseqR'
decompress,Rle-method Methods for Function decompress in Package 'ChIPseqR'
decompress,RLEBindScore-method Extract Read Count and Binding Site Score Representations
decompress,RleList-method Methods for Function decompress in Package 'ChIPseqR'
decompress,RLEReadCounts-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,BindScore-method Class "BindScore"

-- L --

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

-- M --

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

-- N --

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

-- P --

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

-- R --

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

-- T --

tail,BindScore-method Class "BindScore"

-- W --

windowCounts Summarize read counts in a sliding window

-- misc --

[,BindScore,ANY,missing,missing-method Class "BindScore"
[,ReadCounts,ANY,missing,missing-method Class "ReadCounts"
[<-,ReadCounts,ANY,missing-method Class "ReadCounts"
[[,BindScore,ANY,missing-method Class "BindScore"
[[,BindScore,ANY,numeric-method Class "BindScore"
[[,ReadCounts,ANY,missing-method Class "ReadCounts"
[[<-,ReadCounts,ANY,missing-method Class "ReadCounts"