@@ -1,8 +1,8 @@

 Package: QTLExperiment

 Type: Package

-Date: 2022-11-08

+Date: 2023-09-28

 Title: S4 classes for QTL summary statistics and metadata

-Version: 0.99.0

+Version: 0.99.1

 Authors@R: c(

     person("Christina", "Del Azodi", role=c("aut"), email="[email protected]"), 

     person("Davis","McCarthy", role=c("ctb"), email="[email protected]"),

@@ -12,6 +12,8 @@

 #' @name QTLe-coerce

 #' @rdname mash2qtle

 #'

+#' @returns A \linkS4class{QTLExperiment} object.

+#'

 #' @examples

 #' nStates <- 6

 #' nQTL <- 40

@@ -14,9 +14,13 @@

 #' nStates <- 6

 #' nQTL <- 40

 #'

+#' # Mock QTLExperiment data

+#'

 #' qtle <- mockQTLE(nStates, nQTL)

 #' dim(qtle)

 #'

+#' @returns an object containing simulated data.

+#'

 #' @author Christina B Azodi, Amelia Dunstone

 #' @export

 #'

@@ -20,6 +20,8 @@

 #'

 #' @example man/examples/qtle_load_example.R

 #'

+#' @returns A \linkS4class{QTLExperiment} object.

+#'

 #' @author

 #' Christina B Azodi, Amelia Dunstone

 #'

@@ -62,7 +64,7 @@ sumstats2qtle <- function(input, feature_id = "gene_id",

     } else{

         data <- vroom(input$path, id="path", show_col_types = FALSE,

                       n_max = n_max,

-                      col_select=list(path, feature_id = all_of(feature_id),

+                      col_select=list(all_of(path), feature_id = all_of(feature_id),

                                       variant_id = all_of(variant_id),

                                       betas = all_of(betas),

                                       errors = all_of(errors),

@@ -5,6 +5,40 @@

 #'

 #' @param object QTLExperiment object

 #'

+#' @returns A \linkS4class{QTLExperiment} object with recovered rowData or colData.

+#'

+#' @examples

+#'

+#' # Recover a column in colData

+#'

+#' qtle <- mockQTLE()

+#'

+#' head(colData(qtle))

+#'

+#' new_colData <- DataFrame(list(some_info1 = LETTERS[1:ncol(qtle)],

+#'                               some_info2 = c(1:ncol(qtle))))

+#'

+#' # colData is overwritten

+#' colData(qtle) <- new_colData

+#' head(colData(qtle))

+#'

+#' # colData is recovered

+#' qtle <- recover_qtle_ids(qtle)

+#' head(colData(qtle))

+#'

+#' # Recover information from rowData

+#'

+#' head(rowData(qtle))

+#'

+#' # variant_id are shuffled accidentally

+#' rowData(qtle)$variant_id <- sample(rowData(qtle)$variant_id, nrow(qtle))

+#' head(rowData(qtle))

+#'

+#' # Recover rowData

+#' qtle <- recover_qtle_ids(qtle)

+#' head(rowData(qtle))

+#'

+#'

 #' @name QTLe-recover

 #' @rdname recover_qtle_ids

 #' @docType methods

@@ -33,6 +33,8 @@

 #' passed to the corresponding \linkS4class{SummarizedExperiment} method.}

 #' }

 #'

+#' @returns A \linkS4class{QTLExperiment} object.

+#'

 #' @author

 #' Christina B Azodi

 #'

@@ -4,7 +4,7 @@

 #' the class structure. This is usually called by internal methods rather than

 #' by users or downstream packages.

 #'

-#' @param object A old \linkS4class{QTLExperiment} object.

+#' @param object An old \linkS4class{QTLExperiment} object.

 #' @param ... Additional arguments that are ignored.

 #' @param verbose Logical scalar indicating whether a message should be emitted

 #'        as the object is updated.

@@ -19,6 +19,12 @@

 #' @return

 #' An updated version of \code{object}.

 #'

+#' @examples

+#' qtle <- mockQTLE()

+#' objectVersion(qtle)

+#'

+#' qtle_new <- QTLExperiment::updateObject(qtle)

+#'

 #' @author Christina B Azodi

 #'

 #' @seealso

@@ -23,6 +23,9 @@ mash2qtle(data, sep = NULL, rowData = NULL, verbose = FALSE)

 \item{verbose}{Logical.}

 }

+\value{

+A \linkS4class{QTLExperiment} object.

+}

 \description{

 Function to coerce a mashr object (class list or mashr) into a QTLe object.

 }

@@ -23,6 +23,9 @@ mockMASHR_FIT(nStates = 10, nQTL = 100)

 \item{names}{Logical to include column and row names}

 }

+\value{

+an object containing simulated data.

+}

 \description{

 Functions to create fake input data for QTLExperiments.

 }

@@ -30,6 +33,8 @@ Functions to create fake input data for QTLExperiments.

 nStates <- 6

 nQTL <- 40

+# Mock QTLExperiment data

+

 qtle <- mockQTLE(nStates, nQTL)

 dim(qtle)

@@ -11,7 +11,43 @@ recover_qtle_ids(object)

 \arguments{

 \item{object}{QTLExperiment object}

 }

+\value{

+A \linkS4class{QTLExperiment} object with recovered rowData or colData.

+}

 \description{

 Function to recover protected rowData (feature_id, variant_id)

 and colData (state_id) from internal structure.

 }

+\examples{

+

+# Recover a column in colData

+

+qtle <- mockQTLE()

+

+head(colData(qtle))

+

+new_colData <- DataFrame(list(some_info1 = LETTERS[1:ncol(qtle)],

+                              some_info2 = c(1:ncol(qtle))))

+

+# colData is overwritten

+colData(qtle) <- new_colData

+head(colData(qtle))

+

+# colData is recovered

+qtle <- recover_qtle_ids(qtle)

+head(colData(qtle))

+

+# Recover information from rowData

+

+head(rowData(qtle))

+

+# variant_id are shuffled accidentally

+rowData(qtle)$variant_id <- sample(rowData(qtle)$variant_id, nrow(qtle))

+head(rowData(qtle))

+

+# Recover rowData

+qtle <- recover_qtle_ids(qtle)

+head(rowData(qtle))

+

+

+}

@@ -8,6 +8,9 @@

 \alias{[,QTLExperiment,ANY,ANY,ANY-method}

 \alias{[<-,QTLExperiment,ANY,ANY,QTLExperiment-method}

 \title{Subsetting and replacing data in QTLExperiment objects}

+\value{

+A \linkS4class{QTLExperiment} object.

+}

 \description{

 Includes methods to subset a \linkS4class{QTLExperiment} object by

 row and/or column and methods to replace all data for the specified rows

@@ -37,6 +37,9 @@ for testing purposes.}

 \item{verbose}{logical. Whether to print progress messages.}

 }

+\value{

+A \linkS4class{QTLExperiment} object.

+}

 \description{

 A suite of methods to extract QTL mapping summary statistics from common

 QTL workflow output files.

@@ -8,7 +8,7 @@

 \S4method{updateObject}{QTLExperiment}(object, ..., verbose = FALSE)

 }

 \arguments{

-\item{object}{A old \linkS4class{QTLExperiment} object.}

+\item{object}{An old \linkS4class{QTLExperiment} object.}

 \item{...}{Additional arguments that are ignored.}

@@ -29,6 +29,13 @@ internal class representation. Changes are as follows:

 \itemize{

 \item No updates yet.

 }

+}

+\examples{

+qtle <- mockQTLE()

+objectVersion(qtle)

+

+qtle_new <- QTLExperiment::updateObject(qtle)

+

 }

 \seealso{

 \code{\link{objectVersion}}, which is used to determine if the object is up-to-date.