fix a few bugsi

ococrook · May 5, 2024 · b042bd3 · b042bd3
1 parent 352acbf
commit b042bd3
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Showing 2 changed files with 16 additions and 10 deletions.
diff --git a/R/Rex-differential.R b/R/Rex-differential.R
@@ -51,9 +51,9 @@
 ##'
 ##' @export
 processDifferential <- function(HdxData,
-    params,
-    whichChain = 1,
-    num_montecarlo = 5000) {
+                                params,
+                                whichChain = 1,
+                                num_montecarlo = 5000) {
     # check for comptability
     stopifnot(
         "Residues are incompatible between expreiments" =
@@ -125,9 +125,9 @@ processDifferential <- function(HdxData,
 
     Rex.estimates <- DataFrame(
         Residues = Residues,
-        signedARE = t(signedARE),
-        ARE = t(ARE),
-        TRE = t(TRE)
+        signedARE = t(signedARE)[Residues,],
+        ARE = t(ARE)[Residues,],
+        TRE = t(TRE)[Residues,]
     )
 
     colnames(Rex.estimates) <- c(
@@ -142,8 +142,8 @@ processDifferential <- function(HdxData,
 
     Rex.probs <- DataFrame(
         Residues = Residues,
-        probs = t(probs),
-        totalprobs = totalprobs
+        probs = t(probs)[Residues,],
+        totalprobs = totalprobs[Residues]
     )
 
     colnames(Rex.probs) <- c(

diff --git a/R/Rex-error.R b/R/Rex-error.R
@@ -10,6 +10,7 @@
 ##' @return Returns exchange indexes as a list
 ##'
 error_prediction <- function(res, blong, pilong, qlong, dlong, phi) {
+
     timepoints <- unique(res$Exposure)
     out_res <- sapply(seq.int(length(blong)), function(z) {
         doublelogisticFunction(timepoints,
@@ -18,9 +19,14 @@ error_prediction <- function(res, blong, pilong, qlong, dlong, phi) {
             pi = pilong[z], d = dlong[z]
         )
     })
+
     numtimepoints <- length(unique(res$Exposure))
     numRep <- table(res$Sequence)[1] / numtimepoints
-
+
+    min_index <- min(res$Start)
+    max_index <- max(res$End)
+    colnames(out_res) <- seq(min_index, max_index)
+
 
     diff_coupling <- matrix(NA, nrow = length(unique(res$Sequence)), ncol = numtimepoints)
 
@@ -32,7 +38,7 @@ error_prediction <- function(res, blong, pilong, qlong, dlong, phi) {
         seq <- strsplit(unique(res$Sequence)[j], "")[[1]]
         seq <- seq[-c(1:2)]
         index <- which(seq != "P") + start + 1
-        mu <- rowSums(out_res[, index])
+        mu <- rowSums(out_res[, as.character(index)])
 
         diff_coupling[j, ] <- mu - colMeans(matrix(res$Uptake[res$Sequence == unique(res$Sequence)[j]], nrow = numRep))
     }