# CNE Detection and Visualization

## Documentation for package ‘CNEr’ version 1.12.1

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

## Help Pages

A B C F G L M N O P Q R S T U W misc

## -- 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 --

GRangePairs | GRangePairs objects
GRangePairs-class | GRangePairs objects
grangesPairsForDotplot | grangesPairsForDotplot
grglist-method | GRangePairs objects

## -- L --

last | GRangePairs objects
last-method | GRangePairs objects
lastal | lastal wrapper
lastz | lastz wrapper
lavToPsl | lavToPsl
length-method | Class '"Axt"'

## -- 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 --

N50 | Assembly statistics.
N90 | Assembly statistics.
netToAxt | netToAxt

## -- O --

orgKEGGIds2EntrezIDs | 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 --

targetRanges | Class '"Axt"'
targetRanges-method | Class '"Axt"'
targetSeqs | Class '"Axt"'
targetSeqs-method | Class '"Axt"'
thresholds | Class '"CNE"'
thresholds-method | Class '"CNE"'

## -- U --

unique-method | GRangePairs objects
unlist-method | GRangePairs objects

## -- W --

writeAxt | 'writeAxt' function

## -- misc --

[-method | Class '"Axt"'