1. QTLExperiment
  2. man
  3. mash2qtle.Rd
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Improve data loading in sumstats2qtle - When there are multiple p-values for the same test and state, take the mean value

dunstone-a authored on 02/10/2024 12:13:27
Showing 1 changed files
man/mash2qtle.Rd
History View file @ be7a2f0
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@@ -36,8 +36,9 @@ mashr_sim <- mockMASHR(nStates, nQTL)
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 qtle2 <- mash2qtle(
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     mashr_sim,
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-    rowData=DataFrame(feature_id=row.names(mashr_sim$Bhat),
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-                      variant_id=sample(seq_len(nQTL))))
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+    rowData=DataFrame(
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+        feature_id=row.names(mashr_sim$Bhat),
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+        variant_id=sample(seq_len(nQTL))))
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 dim(qtle2)
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Add an example and more return statements

dunstone-a authored on 28/09/2023 12:04:21
Showing 1 changed files
man/mash2qtle.Rd
History View file @ 1f0383d
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@@ -23,6 +23,9 @@ mash2qtle(data, sep = NULL, rowData = NULL, verbose = FALSE)
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 \item{verbose}{Logical.}
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 }
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+\value{
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+A \linkS4class{QTLExperiment} object.
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+}
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 \description{
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 Function to coerce a mashr object (class list or mashr) into a QTLe object.
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 }
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Add examples for some functions - mock data functions - mashr to QTLE conversion function

Amelia Dunstone authored on 27/09/2023 03:20:50
Showing 1 changed files
man/mash2qtle.Rd
History View file @ b2e746f
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@@ -25,7 +25,20 @@ mash2qtle(data, sep = NULL, rowData = NULL, verbose = FALSE)
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 }
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 \description{
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 Function to coerce a mashr object (class list or mashr) into a QTLe object.
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+}
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+\examples{
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+nStates <- 6
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+nQTL <- 40
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+mashr_sim <- mockMASHR(nStates, nQTL)
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+
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+qtle2 <- mash2qtle(
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+    mashr_sim,
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+    rowData=DataFrame(feature_id=row.names(mashr_sim$Bhat),
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+                      variant_id=sample(seq_len(nQTL))))
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+dim(qtle2)
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+
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+
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 }
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 \author{
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-Christina B Azodi
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+Christina B Azodi, Amelia Dunstone
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 }
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adding CI/CD

cazodi authored on 07/11/2022 20:31:15
Showing 1 changed files
man/mash2qtle.Rd
History View file @ 5c5e2a1
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new file mode 100644
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@@ -0,0 +1,31 @@
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+% Generated by roxygen2: do not edit by hand
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+% Please edit documentation in R/mash_2_qtle.R
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+\docType{methods}
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+\name{QTLe-coerce}
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+\alias{QTLe-coerce}
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+\alias{mash2qtle}
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+\alias{.mashData_2_qtle}
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+\alias{.mashFit_2_qtle}
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+\title{Coercing mash data objects into QTLe objects}
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+\usage{
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+mash2qtle(data, sep = NULL, rowData = NULL, verbose = FALSE)
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+
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+.mashData_2_qtle(data)
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+
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+.mashFit_2_qtle(data)
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+}
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+\arguments{
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+\item{data}{A mashr object output from mash_set_data() or mash() from mashr.}
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+
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+\item{sep}{String separating the feature_id from the variant_id in the row.names of the mashr object}
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+
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+\item{rowData}{if feature_id and variant_id are not in the row.names, a rowData matrix can be provided with this information.}
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+
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+\item{verbose}{Logical.}
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+}
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+\description{
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+Function to coerce a mashr object (class list or mashr) into a QTLe object.
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+}
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+\author{
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+Christina B Azodi
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+}