CNE Detection and Visualization

Documentation for package ‘CNEr’ version 1.12.1

Help Pages

-- A --

axisTrack	Example data for plotting annotation.
Axt	Class '"Axt"'
Axt-class	Class '"Axt"'
axtChain	axtChain
axtInfo	axtInfo function

-- B --

binFromCoordRange	UCSC bin indexing system utility functions
binRangesFromCoordRange	UCSC bin indexing system utility functions
binRestrictionString	UCSC bin indexing system utility functions
blatCNE	Wrapper function of blat for 'CNE' object

-- C --

c-method	Class '"Axt"'
c-method	GRangePairs objects
ceScan	ceScan function
ceScan-method	ceScan function
chainMergeSort	chainMergeSort
chainNetSyntenic	chainNetSyntenic
chainPreNet	chainPreNet
class:GRangePairs	GRangePairs objects
CNE	Class '"CNE"'
CNE-class	Class '"CNE"'
CNE12	Class '"CNE"'
CNE12-method	Class '"CNE"'
CNE21	Class '"CNE"'
CNE21-method	Class '"CNE"'
CNEDanRer10Hg38	CNEHg38DanRer10 and CNEDanRer10Hg38 dataset
CNEDensity	CNEDensity function
CNEDensity-method	CNEDensity function
CNEDensity-methods	CNEDensity function
CNEFinal	Class '"CNE"'
CNEFinal-method	Class '"CNE"'
cneFinalListDanRer10Hg38	cneFinalListDanRer10Hg38 dataset
CNEHg38DanRer10	CNEHg38DanRer10 and CNEDanRer10Hg38 dataset
cneMerge	CNE merge function
cneMerge-method	CNE merge function
CNEMerged	Class '"CNE"'
CNEMerged-method	Class '"CNE"'
coerce-method	GRangePairs objects
cpgIslands	Example data for plotting annotation.

-- F --

fetchChromSizes	fetchChromSizes function.
first-method	GRangePairs objects
fixCoordinates	Fix the coordinates in 'Axt' object
fixCoordinates-method	Fix the coordinates in 'Axt' object

-- G --

-- L --

-- M --

makeAncoraFiles	makeAncoraFiles
makeAxtTracks	makeAxtTracks
makeCNEDensity	Make 'Bed', 'bedGraph' and 'BigWig' files
makeGRBs	makeGRBs
matchDistribution	Plot the distribution of matched alignments.
matchDistribution-method	Plot the distribution of matched alignments.

-- N --

-- O --

Fetch mapping from KEGG IDs to Entrez IDs

-- P --

plotCNEDistribution	Plot sequential CNE number against CNE genomic location
plotCNEWidth	Plot the CNE widths distribution
psubAxt	Parallel subset of Axt alignment

-- Q --

queryCNEData	Query the CNEData package to fetch the CNEs
queryRanges	Class '"Axt"'
queryRanges-method	Class '"Axt"'
querySeqs	Class '"Axt"'
querySeqs-method	Class '"Axt"'

-- R --

read.rmMask.GRanges	Read a RepeatMasker .out file
read.rmskFasta	Read a soft repeat masked fasta
readAncora	Read the cne file from Ancora format.
readAncoraIntoSQLite	Read Ancora legacy CNE format
readAxt	Read 'Axt' file
readBed	Read bed file
readCNERangesFromSQLite	readCNERangesFromSQLite function
refGenes	Example data for plotting annotation.
reverseCigar	reverseCigar function

-- S --

saveCNEToSQLite	Save CNE to SQLite
score-method	Class '"Axt"'
scoringMatrix	scoringMatrix
second-method	GRangePairs objects
seqinfo-method	GRangePairs objects
seqnames-method	GRangePairs objects
strand-method	GRangePairs objects
subAxt	Subset an 'Axt' object
subAxt-method	Subset an 'Axt' object
subAxt-methods	Subset an 'Axt' object
summary	Utility functions related to Axt alignment
summary-method	Utility functions related to Axt alignment
swap	GRangePairs objects
swap-method	GRangePairs objects
symCount	Class '"Axt"'
symCount-method	Class '"Axt"'
syntenicDotplot	Syntenic dotplot
syntenicDotplot-method	Syntenic dotplot

-- T --

-- U --

unique-method	GRangePairs objects
unlist-method	GRangePairs objects

-- W --

'writeAxt' function

-- misc --

Class '"Axt"'