CNE Detection and Visualization


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Documentation for package ‘CNEr’ version 1.40.0

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

-- A --

addAncestorGO Add ancestor GO IDs
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"'