Nothing
strCompare <- function(ctFile1,ctFile2,randomTime = 1000){
if(dim(ctFile1)[1] >= dim(ctFile2)[1]){
RNAstructure1 <- ctFile1
RNAstructure2 <- ctFile2
}else{
RNAstructure1 <- ctFile2
RNAstructure2 <- ctFile1
}
###
h1 <- hairpin_loop(RNAstructure1)
hairpin_loop_1 <- unlist(h1)
h1Num <- length(h1)
h2 <- hairpin_loop(RNAstructure2)
hairpin_loop_2 <- unlist(h2)
h2Num <- length(h2)
i1 <- internal_loop(RNAstructure1)
internal_loop_1 <- unlist(i1)
i1Num <- length(i1)
i2 <- internal_loop(RNAstructure2)
internal_loop_2 <- unlist(i2)
i2Num <- length(i2)
b1 <- bulge_loop(RNAstructure1)
bulge_loop_1 <- unlist(b1)
b1Num <- length(b1)
b2 <- bulge_loop(RNAstructure2)
bulge_loop_2 <- unlist(b2)
b2Num <- length(b2)
m1 <- multi_branch_loop(RNAstructure1)
multi_branch_loop_1 <- unlist(m1)
m1Num <- length(m1)
m2 <- multi_branch_loop(RNAstructure2)
multi_branch_loop_2 <- unlist(m2)
m2Num <- length(m2)
s1 <- stem(RNAstructure1)
stem_1 <- unlist(s1)
s1Num <- length(s1)
s2 <- stem(RNAstructure2)
stem_2 <- unlist(s2)
s2Num <- length(s2)
e1 <- external_loop(RNAstructure1)
external_loop1 <- unlist(e1)
e1Num <- length(e1)
e2 <- external_loop(RNAstructure2)
external_loop2 <- unlist(e2)
e2Num <- length(e2)
###
seqCode1 <- ""
for(index1 in 1:dim(RNAstructure1)[1]){
if(index1 %in% hairpin_loop_1){
seqCode1 <- paste0(seqCode1,"H")
}else if(index1 %in% bulge_loop_1){
seqCode1 <- paste0(seqCode1,"B")
}else if(index1 %in% internal_loop_1){
seqCode1 <- paste0(seqCode1,"I")
}else if(index1 %in% multi_branch_loop_1){
seqCode1 <- paste0(seqCode1,"M")
}else if(index1 %in% stem_1){
if(RNAstructure1[index1,5] > RNAstructure1[index1,6]){
seqCode1 <- paste0(seqCode1,"s")
}else{
seqCode1 <- paste0(seqCode1,"S")
}
}else{
seqCode1 <- paste0(seqCode1,"E")
}
}
seqCode2 <- ""
for(index2 in 1:dim(RNAstructure2)[1]){
if(index2 %in% hairpin_loop_2){
seqCode2 <- paste0(seqCode2,"H")
}else if(index2 %in% bulge_loop_2){
seqCode2 <- paste0(seqCode2,"B")
}else if(index2 %in% internal_loop_2){
seqCode2 <- paste0(seqCode2,"I")
}else if(index2 %in% multi_branch_loop_2){
seqCode2 <- paste0(seqCode2,"M")
}else if(index2 %in% stem_2){
if(RNAstructure2[index2,5] > RNAstructure2[index2,6]){
seqCode2 <- paste0(seqCode2,"s")
}else{
seqCode2 <- paste0(seqCode2,"S")
}
}else{
seqCode2 <- paste0(seqCode2,"E")
}
}
###
seqA <- RNAstructure1[,2]
seqB <- RNAstructure2[,2]
result0 <- getScore(h1,i1,b1,m1,s1,e1,
seqA,seqCode1,h1Num,i1Num,b1Num,m1Num,s1Num,e1Num,
h2,i2,b2,m2,s2,e2,
seqB,seqCode2,h2Num,i2Num,b2Num,m2Num,s2Num,e2Num)
arrSimilarity <- c()
for(i in 1:randomTime){
randomSeq1 <- sample(strsplit(seqCode1,split = "")[[1]],nchar(seqCode1))
seqCode1 <- paste(randomSeq1,sep = "",collapse = "")
randomSeq2 <- sample(strsplit(seqCode2,split = "")[[1]],nchar(seqCode2))
seqCode2 <- paste(randomSeq2,sep = "",collapse = "")
result <- getScore(h1,i1,b1,m1,s1,e1,
seqA,seqCode1,h1Num,i1Num,b1Num,m1Num,s1Num,e1Num,
h2,i2,b2,m2,s2,e2,
seqB,seqCode2,h2Num,i2Num,b2Num,m2Num,s2Num,e2Num)
arrSimilarity <- c(arrSimilarity,result$Similarity)
}
pValue <- 1 - pnorm(result0$Similarity,mean = mean(arrSimilarity),sd = sd(arrSimilarity))
result2 <- list("Similarity" = result0$Similarity,"Pvalue" = pValue,
"longSeq" = result0$longSeq,"shortSeq" = result0$shortSeq,
"longSeqCode" = result0$longSeqCode,"shortSeqCode" = result0$shortSeqCode)
###################
return(result2)
}
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.