dNdScv_test.R

library("seqinr")
library("Biostrings")
library("MASS")
library("GenomicRanges")
library("dndscv")

## Helper methods copied from dndscv
nt = c("A","C","G","T")
compnt = setNames(rev(nt), nt)

chr2cds = function(pos,cds_int,strand) {
  if (strand==1) {
    return(which(pos==unlist(apply(cds_int, 1, function(x) x[1]:x[2]))))
  } else if (strand==-1) {
    return(which(pos==rev(unlist(apply(cds_int, 1, function(x) x[1]:x[2])))))
  }
}

rest_nt <- function(n) {
  rest_nts <- nt[-which(nt == n)]
  
  sample(rest_nts, 1)
}

data("refcds_hg19", package="dndscv")

TP53 <- RefCDS[which(sapply(RefCDS, function(x) x$gene_name) == "TP53")]

cds_int <- TP53[[1]]$intervals_cds
cds_pos <- unlist(apply(cds_int, 1, function(x) x[1]:x[2]))
splice_pos <- TP53[[1]]$intervals_splice

# Use mutations from example dataset but remove all mapping to TP53
data("dataset_simbreast", package="dndscv")
my_mutations <- subset(mutations, !(chr == "17" & pos %in% cds_pos) & nchar(ref) == 1 & !(pos %in% splice_pos))

# Sample 50 random positions in the TP53 CDS
my_mut_pos <- sample(cds_pos, 50)

# Make a data frame with random mutations at sampled positions
my_mut_cds_pos <- sapply(my_mut_pos, function(x) (chr2cds(x, TP53[[1]]$intervals_cds, TP53[[1]]$strand)))
my_mut_ref <- sapply(my_mut_cds_pos,
                     function(x) as.character(TP53[[1]]$seq_cds[x]))
my_muts <- data.frame(sampleID=paste0("S_", 1:length(my_mut_pos)),
                      chr=TP53[[1]]$chr,pos=my_mut_pos,
                      ref=compnt[my_mut_ref],
                      mut=sapply(my_mut_ref, rest_nt),
                      stringsAsFactors=F)

## Apply dndscv on the combined mutations
dndsout = dndscv(rbind(my_mutations[, 1:5], my_muts))

sel_cv = dndsout$sel_cv
signif_genes = sel_cv[sel_cv$qglobal_cv<0.1, c("gene_name","qglobal_cv")]
rownames(signif_genes) = NULL
print(signif_genes)