#'@description Counts how many sequencing points were at known genes
#'
#'@title matchToGene
#'
#'@param positions positions from sequencing
#'@param start gene start index
#'@param stop gene stop index
#'@param geneName gene name
#'@param range how many nucleotide before \code{start} and after \code{stop} we include to genes
#'
#'
#'@importFrom dplyr between
#'@export
matchToGene <- function(positions, start, stop, geneName, range=0){
geneName <- geneName
nrow <- length(geneName)
counts <- as.data.frame(matrix(nrow=nrow,ncol=2))
colnames(counts)<-c("count","name")
if(range>0){
start <- start-range
stop <- stop+range
}
for (i in 1:length(start)){
points <- positions[between(positions, start[i], stop[i])]
counts$count[i]<-length(points)
}
counts$name <- geneName
return(counts)
}
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