@@ -1,6 +1,6 @@

 Package: crisprScore

-Version: 1.3.1

-Date: 2022-10-17

+Version: 1.3.2

+Date: 2023-04-03

 Title: On-Target and Off-Target Scoring Algorithms for CRISPR gRNAs

 Authors@R: c(

     person("Jean-Philippe", "Fortin", email = "[email protected]", role = c("aut", "cre", "cph")),

@@ -98,7 +98,7 @@ getMITScores <- function(spacers,

         } else {

             d <- (max(indices)-min(indices))/(m-1)

         }

-        t1 <- prod(mit.weights[as.character(indices)])

+        t1 <- prod(1-mit.weights[as.character(indices)])

         t2 <- 1/(m^2)

         t3 <- 1/((19-d)/19*4+1)

         if (includeDistance){

@@ -2,6 +2,12 @@

 \title{crisprScore News}

 \encoding{UTF-8}

+

+\section{Version 1.3.1}{\itemize{

+\item Fixed MIT formula. Previous calculations were erroneous. 

+}}

+

+

 \section{Version 1.0.0}{\itemize{

 \item New package \pkg{crisprScore}, for on-target and off-target scoring of guide RNAs (gRNAs).

 }}

\ No newline at end of file

Binary files a/inst/mit/mit.weights.rda and b/inst/mit/mit.weights.rda differ

@@ -1,7 +1,7 @@

 ws <- read.table("mit.weights.txt", head=TRUE)$w

-names(ws) <- 20:1

+names(ws) <- 1:20

 mit.weights <- ws

 mit.weights <- mit.weights[order(as.numeric(names(mit.weights)))]

 save(mit.weights, file="mit.weights.rda")

-#Higher scores indicate greater mismatch tolerance

-#Positions are 5' to 3' (pos20 = most PAM-adjacent position)

+#Scores of 0 indicate perfect mismatch tolerance

+#Positions are already 5' to 3' (pos20 = most PAM-adjacent position)

@@ -11,7 +11,7 @@ protospacers_cas9 <- c("ATCGATGCTGATGCTAGATA",

 pam_cas9 <- c("AGG","AAG", "AGA", "AGT", "AGG", "AGG", "AGG")

 #dput(round(getMITScores(spacer, protospacers)$score,3))

 #dput(round(getCFDScores(spacer, protospacers)$score,3))

-mit_scores <- c(1, 0.259, 0.069, 0.016, 0.583, 0, 0)

+mit_scores      <- c(1, 0.259, 0.069, 0.016, 0.417, 0.104, 0.004)

 cfd_scores_cas9 <- c(1, 0.259, 0.069, 0.016, 1, 0.765, 0.301)