- due to changes in struct (removal of unicode)
Gavin Rhys Lloyd authored on 02/02/2024 10:50:50
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@@ -24,7 +24,7 @@ The samples in the data matrix are normalised to account for differences in conc |
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\section{Inheritance}{
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A \code{vec_norm} object inherits the following \code{struct} classes: \cr\cr
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-\code{vec_norm()} ⭢ \code{model()} ⭢ \code{struct_class()}
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+\verb{[vec_norm]} >> \verb{[model]} >> \verb{[struct_class]}
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} |
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\examples{
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- get_description moved to struct and updated
Gavin Rhys Lloyd authored on 31/01/2024 09:48:31
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@@ -21,7 +21,15 @@ struct object |
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\description{
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The samples in the data matrix are normalised to account for differences in concentration by scaling each sample such that the sum of squares is equal to 1. |
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} |
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+\section{Inheritance}{
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+ |
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+A \code{vec_norm} object inherits the following \code{struct} classes: \cr\cr
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+\code{vec_norm()} ⭢ \code{model()} ⭢ \code{struct_class()}
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+} |
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+ |
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\examples{
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M = vec_norm() |
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+M = vec_norm() |
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+ |
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} |
Gavin Rhys Lloyd authored on 07/07/2021 09:37:19
• GitHub committed on 07/07/2021 09:37:19
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@@ -10,7 +10,11 @@ vec_norm(...) |
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\item{...}{Additional slots and values passed to \code{struct_class}.}
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} |
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\value{
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-A \code{vec_norm} object.
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+A \code{vec_norm} object with the following \code{output} slots:
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+\tabular{ll}{
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+\code{normalised} \tab (DatasetExperiment) A DatasetExperiment object containing the normalised data. \cr
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+\code{coeff} \tab (data.frame) The normalisation coefficients calculated by PQN. \cr
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+} |
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struct object |
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} |
* fix base=10 regardless of input (see #15)
class constructor was always setting base to 10 instead of the input value
* merge bug fix 1.01 into dev (#19)
* bug fix issue #7
Correctly re-order the sample_meta column for colouring samples in the dendrogram plot
* version bump
bug fix issue #7
* fix for https://github.com/computational-metabolomics/structToolbox/issues/18 (#20)
correctly reorder the factor labels so that the control group always ends up in the denominator for the fold change calculation.
* fix for https://github.com/computational-metabolomics/structToolbox/issues/18
fixed incorrect length check on matching class labels.
* Issue 17 ttest factor (#21)
* convert to factor if not one already
fix for issue #17
* update roxygen version
* fix for issue #9 (#22)
changed from lapply to vapply and used drop=FALSE to ensure compatibility with a single factor.
* allow user to set lambda (#24)
- lambda changed to input parameter. NULL = uses pmp optimisation
- model_predict now uses the set value of lambda, or lambda_opt if used.
- documentation updated
* Feature non parametric fold change (#26)
* add "median" method
based on DOI: 10.1080/00949650212140 can now calcuate fold changes equivalent to using medians and corresponding confidence intervals
* update documentation
* update median method
now correctly calculates ratio of medians
* use wilcox for paired median intervals
make use of wilcox.test to estimate intervals for the median when using median for paired samples
* Issue 23 filter by name (#27)
* fix for #23
moved all model_apply functionality to model_predict so that model_train and model_predict can be used as well as model_apply
* update documentation
* Update mean_of_medians.R (#29)
fix for #28
- correctly loop over all levels in the named factor
* Feature documentation 3 12 (#31)
* update documentation
Description and inputs now pulled from the object definitions for consistency.
* fix definition of label_features
allows NULL and description updated
* replace non ascii characters
* export mixed_effect object
* use correct object name to generate documentation
* export mixed_effect object
* remove non ascii characters
* update tests with new object name
* add import for capture.output
* add import for capture.output
* use pca_biplot in tests
chart was renamed
* add utils import
* update struct dependency version
* update documentation
* update news, version bump
Gavin Rhys Lloyd authored on 25/10/2020 08:50:13
• GitHub committed on 25/10/2020 08:50:13
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@@ -7,14 +7,15 @@ |
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vec_norm(...) |
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} |
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\arguments{
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-\item{...}{additional slots and values passed to struct_class}
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+\item{...}{Additional slots and values passed to \code{struct_class}.}
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} |
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\value{
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+A \code{vec_norm} object.
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+ |
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struct object |
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} |
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\description{
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-Applies vector normalisation, such the sum of squared values for each sample |
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-after normalisation are equal to 1. |
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+The samples in the data matrix are normalised to account for differences in concentration by scaling each sample such that the sum of squares is equal to 1. |
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} |
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\examples{
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M = vec_norm() |
Gavin Rhys Lloyd authored on 06/02/2020 13:51:52
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@@ -2,7 +2,7 @@ |
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% Please edit documentation in R/vec_norm_class.R |
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\name{vec_norm}
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\alias{vec_norm}
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-\title{vector nromalisation}
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+\title{Vector normalisation}
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\usage{
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vec_norm(...) |
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} |
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@@ -13,7 +13,8 @@ vec_norm(...) |
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struct object |
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} |
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\description{
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-applies vector normalisation |
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+Applies vector normalisation, such the sum of squared values for each sample |
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+after normalisation are equal to 1. |
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} |
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\examples{
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M = vec_norm() |
Gavin Rhys Lloyd authored on 04/02/2020 17:18:11
Gavin Rhys Lloyd authored on 19/12/2019 15:14:02
...update some documentation
Gavin Rhys Lloyd authored on 17/12/2019 17:24:38
...rename all function with dot to underscore
replace dataset with DatasetExperiment
Gavin Rhys Lloyd authored on 17/12/2019 15:48:01
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new file mode 100644 |
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@@ -0,0 +1,15 @@ |
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+% Generated by roxygen2: do not edit by hand |
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+% Please edit documentation in R/vec_norm_class.R |
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+\name{vec_norm}
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+\alias{vec_norm}
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+\title{vector nromalisation}
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+\usage{
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+vec_norm(...) |
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+} |
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+\description{
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+applies vector normalisation |
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+} |
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+\examples{
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+M = vec_norm() |
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+ |
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+} |