@@ -46,16 +46,19 @@

 #' betas <- matrix(rnorm(nStates * nQTL), ncol=nStates)

 #' error <- matrix(abs(rnorm(nStates * nQTL)), ncol=nStates)

 #'

-#' qtle <- QTLExperiment(assays=list(betas=betas, errors=error),

-#'                       feature_id=sample(1:10, nQTL, replace=TRUE),

-#'                       variant_id=sample(seq(1e3:1e5), nQTL),

-#'                       state_id=LETTERS[1:nStates])

+#' qtle <- QTLExperiment(

+#'     assays=list(betas=betas, errors=error),

+#'     feature_id=sample(1:10, nQTL, replace=TRUE),

+#'     variant_id=sample(seq(1e3:1e5), nQTL),

+#'     state_id=LETTERS[1:nStates])

 #' qtle

 #'

 #' ## coercion from SummarizedExperiment

 #' mock_sumstats <- mockSummaryStats(nStates=10, nQTL=100)

-#' se <- SummarizedExperiment(assays=list(betas=mock_sumstats$betas,

-#'                                        errors=mock_sumstats$errors))

+#' se <- SummarizedExperiment(

+#'     assays=list(

+#'         betas=mock_sumstats$betas,

+#'         errors=mock_sumstats$errors))

 #' as(se, "QTLExperiment")

 #'

 #' @docType class

@@ -21,8 +21,9 @@

 #'

 #' qtle2 <- mash2qtle(

 #'     mashr_sim,

-#'     rowData=DataFrame(feature_id=row.names(mashr_sim$Bhat),

-#'                       variant_id=sample(seq_len(nQTL))))

+#'     rowData=DataFrame(

+#'         feature_id=row.names(mashr_sim$Bhat),

+#'         variant_id=sample(seq_len(nQTL))))

 #' dim(qtle2)

 #'

 #'

@@ -76,11 +76,11 @@ sumstats2qtle <- function(

         fmutate(id=paste0(feature_id, "|", variant_id))

     betas <- data %>% 

-        pivot_wider(names_from=state, values_from=betas, id_cols=id) %>%

+        pivot_wider(names_from=state, values_from=betas, values_fn=mean, id_cols=id) %>%

         tibble::column_to_rownames(var="id") %>% qDF()

     errors <- data %>% 

-        pivot_wider(names_from=state, values_from=errors, id_cols=id) %>%

+        pivot_wider(names_from=state, values_from=errors, values_fn=mean, id_cols=id) %>%

         tibble::column_to_rownames(var="id") %>% qDF()

     object <- QTLExperiment(

@@ -94,7 +94,7 @@ sumstats2qtle <- function(

     if(!is.null(pvalues)){

         pvalues <- data %>% 

-            pivot_wider(names_from=state, values_from=pvalues, id_cols=id) %>%

+            pivot_wider(names_from=state, values_from=pvalues, values_fn=mean, id_cols=id) %>%

             tibble::column_to_rownames(var="id") %>% qDF()

         assay(object, "pvalues") <- pvalues

@@ -24,7 +24,7 @@

 #'

 #' \describe{

 #' \item{\code{x[i, j, ...] <- value}:}{Replaces all data for rows \code{i} and

-#' columns {j} with the corresponding fields in a QTLExperiment

+#' columns \code{j} with the corresponding fields in a QTLExperiment

 #' \code{value}, where \code{i} and \code{j} can be a logical, integer, or

 #' character vector of subscripts, indicating the rows and columns,

 #' respectively, to retain. If either \code{i} or \code{j} is missing, than

@@ -64,16 +64,19 @@ nQTL <- 100

 betas <- matrix(rnorm(nStates * nQTL), ncol=nStates)

 error <- matrix(abs(rnorm(nStates * nQTL)), ncol=nStates)

-qtle <- QTLExperiment(assays=list(betas=betas, errors=error),

-                      feature_id=sample(1:10, nQTL, replace=TRUE),

-                      variant_id=sample(seq(1e3:1e5), nQTL),

-                      state_id=LETTERS[1:nStates])

+qtle <- QTLExperiment(

+    assays=list(betas=betas, errors=error),

+    feature_id=sample(1:10, nQTL, replace=TRUE),

+    variant_id=sample(seq(1e3:1e5), nQTL),

+    state_id=LETTERS[1:nStates])

 qtle

 ## coercion from SummarizedExperiment

 mock_sumstats <- mockSummaryStats(nStates=10, nQTL=100)

-se <- SummarizedExperiment(assays=list(betas=mock_sumstats$betas,

-                                       errors=mock_sumstats$errors))

+se <- SummarizedExperiment(

+    assays=list(

+        betas=mock_sumstats$betas,

+        errors=mock_sumstats$errors))

 as(se, "QTLExperiment")

 }

@@ -36,8 +36,9 @@ mashr_sim <- mockMASHR(nStates, nQTL)

 qtle2 <- mash2qtle(

     mashr_sim,

-    rowData=DataFrame(feature_id=row.names(mashr_sim$Bhat),

-                      variant_id=sample(seq_len(nQTL))))

+    rowData=DataFrame(

+        feature_id=row.names(mashr_sim$Bhat),

+        variant_id=sample(seq_len(nQTL))))

 dim(qtle2)

@@ -38,7 +38,7 @@ In the following, \code{x} is a \linkS4class{QTLExperiment} object.

 \describe{

 \item{\code{x[i, j, ...] <- value}:}{Replaces all data for rows \code{i} and

-columns {j} with the corresponding fields in a QTLExperiment

+columns \code{j} with the corresponding fields in a QTLExperiment

 \code{value}, where \code{i} and \code{j} can be a logical, integer, or

 character vector of subscripts, indicating the rows and columns,

 respectively, to retain. If either \code{i} or \code{j} is missing, than

@@ -1,4 +1,4 @@

-# Setting up the options for a mock MultiStateQTLExperiment.

+# Setting up the options for a mock QTLExperiment

 set.seed(42)

 nQTL <- 100