readCNERangesFromSQLite {CNEr} | R Documentation |
Query the SQLite database based on chromosome,
coordinates and some other criteria.
Primarily not intended to be used directly.
For the CNE density plot, fetchCNEDensity
function should be used.
readCNERangesFromSQLite(dbName, tableName, chr=NULL, start=NULL, end=NULL, whichAssembly=c("first","second"), minLength=NULL, tAssemblyFn=NULL, qAssemblyFn=NULL)
dbName |
A object of |
tableName |
A object of |
chr |
|
start, end |
|
whichAssembly |
|
minLength |
|
tAssemblyFn,qAssemblyFn |
|
An object of GRangePairs
is returned.
Ge Tan
dbName <- file.path(system.file("extdata", package="CNEr"), "danRer10CNE.sqlite") tableName <- "danRer10_hg38_45_50" qAssemblyFn <- file.path(system.file("extdata", package="BSgenome.Hsapiens.UCSC.hg38"), "single_sequences.2bit") tAssemblyFn <- file.path(system.file("extdata", package="BSgenome.Drerio.UCSC.danRer10"), "single_sequences.2bit") ## single chr, start, end chr <- "chr6" start <- 24000000L end <- 27000000 minLength <- 50L fetchedCNERanges <- readCNERangesFromSQLite(dbName, tableName, chr, start, end, whichAssembly="first", minLength=minLength, tAssemblyFn=tAssemblyFn, qAssemblyFn=qAssemblyFn) ## multiple chr, start, end chr=c("chr1", "chr3") start=c(90730248, 137523122) end=c(90730300, 137523190) fetchedCNERanges <- readCNERangesFromSQLite(dbName, tableName, chr, start, end, whichAssembly="second", minLength=minLength) ## chr, NULL, NULL fetchedCNERanges <- readCNERangesFromSQLite(dbName, tableName, chr, start=NULL, end=NULL, whichAssembly="second", minLength=minLength)