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### -----------------------------------------------------------------
### Fetch the CNE coordinates from SQL and compute the densities
### Exported!
CNEDensity <- function(dbName, tableName, chr, start, end,
whichAssembly=c("first", "second"),
windowSize=300, minLength=NULL){
.CNEDensityInternal(dbName=dbName, tableName=tableName,
whichAssembly=whichAssembly,
chr=chr, start=start, end=end,
windowSize=windowSize, minLength=minLength)
}
.CNEDensityInternal <- function(dbName, tableName,
whichAssembly=c("first","second"),
chr, start, end, windowSize,
minLength=NULL){
nrGraphs <- 1
CNEstart <- start
CNEend <- end
stopifnot(length(CNEstart) == 1L)
stopifnot(length(CNEend) == 1L)
# This is the pipeline of doing the density plot
# The windowSize is in kb.
whichAssembly <- match.arg(whichAssembly)
windowSize <- as.integer(windowSize) * 1000
# make things easier
if(windowSize %% 2 == 0)
windowSize <- windowSize - 1L
context_start <- as.integer(max(CNEstart - (windowSize-1L)/2, 1))
context_end <- as.integer(CNEend + (windowSize-1)/2)
rangesPair <- readCNERangesFromSQLite(dbName, tableName, chr,
context_start, context_end,
whichAssembly, minLength)
## When no CNEs are returned
if(length(rangesPair) == 0L){
ans <- GRanges(seqnames=chr,
ranges=IRanges(start=context_start,
end=context_end),
strand="*",
score=0)
return(ans)
}
if(whichAssembly == "first"){
ranges <- first(rangesPair)
}else if(whichAssembly == "second"){
ranges <- second(rangesPair)
}
# Implement get_cne_ranges_in_region_partitioned_by_other_chr later!!!
ranges <- reduce(ranges)
covAll <- coverage(ranges, width=context_end)
runMeanAll <- suppressWarnings(runmean(covAll, k=windowSize, "constant"))
ans <- as(runMeanAll, "GRanges")
ans$score <- ans$score * 100
return(ans)
}
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