altMH <- function(MHSeq_out, index_out){
# this function takes as arguments the MH sequence to look for
# from MHSeq.return and index_out from index
#' @importFrom Biostrings countPattern
NULL
# extract the variables to compare
testSeq <- index_out$delSeq
refSeq <- index_out$refSeq
MH <- MHSeq_out
Del_index <- index_out$delInd
# L and R read position end points
Del_index_L <- min(index_out$delInd)
Del_index_R <- max(index_out$delInd)
# convert and get the DNA sequences using biostrings
# subset the sequence to get deleted sequence from Reference
refDel <- subseq(DNAString(refSeq), start=Del_index_L, end=Del_index_R)
# count the MH pattern in the del sequence # subtract 1 to account for its presence once as the MH quantified initially
altMH_out <- countPattern(MH,refDel)-1
return(altMH_out)
}
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