#' matchLSjunc
#' match the junction site between long reads and short reads
#'
#' @param LRjunc a list of data frame, indicating the splicing junction sites
#' obtained from long reads
#' @param SRjunc a list of data frame, indicating the splicing junction sites
#' obtained from short reads
#'
#' @return a list of data frame for the junction sites of each chromosome. The
#' data frame indicates the locations of junction sites and the
#' correspoding read count from both long and short reads
#'
#' @export
#'
#' @examples
matchLSjunc = function( LRjunc , SRjunc )
{
CHR = intersect( names(SRjunc) , names(LRjunc) )
matched = foreach( k=1:length(CHR) ) %dopar%
{
chr = CHR[k]
cat(chr,"\n")
lrc = LRjunc[[chr]]
src = SRjunc[[chr]]
SRmatch = matrix( ncol=2 , nrow=nrow(lrc) , data=0 )
colnames(SRmatch) = c( "SRindex" , "LSdis" )
for(i in 1:nrow(lrc))
{
dis = abs(src$start-lrc$start[i]) + abs(src$end-lrc$end[i])
ind = which.min(dis)
min = dis[ind]
SRmatch[i,] = c(ind,min)
}
SRmatch
}
names(matched) = CHR
matched
}
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