- due to changes in struct (removal of unicode)
Gavin Rhys Lloyd authored on 02/02/2024 10:50:50
| ... | ... |
@@ -47,7 +47,7 @@ Fold change is the relative change in mean (or non-parametric equivalent) intens |
| 47 | 47 |
\section{Inheritance}{
|
| 48 | 48 |
|
| 49 | 49 |
A \code{fold_change} object inherits the following \code{struct} classes: \cr\cr
|
| 50 |
-\code{fold_change()} ⭢ \code{model()} ⭢ \code{struct_class()}
|
|
| 50 |
+\verb{[fold_change]} >> \verb{[model]} >> \verb{[struct_class]}
|
|
| 51 | 51 |
} |
| 52 | 52 |
|
| 53 | 53 |
\examples{
|
- get_description moved to struct and updated
Gavin Rhys Lloyd authored on 31/01/2024 09:48:31
| ... | ... |
@@ -18,17 +18,17 @@ fold_change( |
| 18 | 18 |
\arguments{
|
| 19 | 19 |
\item{factor_name}{(character) The name of a sample-meta column to use.}
|
| 20 | 20 |
|
| 21 |
-\item{paired}{(logical) Paired fold change. Allowed values are limited to the following: \itemize{\item{\code{"TRUE"}: Fold change is calculated taking into account paired sampling.}\item{\code{"FALSE"}: Fold change is calculated assuming there is no paired sampling.}} The default is \code{FALSE}.}
|
|
| 21 |
+\item{paired}{(logical) Paired fold change. Allowed values are limited to the following: \itemize{ \item{\code{"TRUE"}: Fold change is calculated taking into account paired sampling.}\item{\code{"FALSE"}: Fold change is calculated assuming there is no paired sampling.}} The default is \code{FALSE}.\cr}
|
|
| 22 | 22 |
|
| 23 | 23 |
\item{sample_name}{(character) The name of a sample_meta column containing sample identifiers for paired sampling. The default is \code{character(0)}.}
|
| 24 | 24 |
|
| 25 |
-\item{threshold}{(numeric) The fold change threshold for labelling features as significant. The default is \code{2}.}
|
|
| 25 |
+\item{threshold}{(numeric) The fold change threshold for labelling features as significant. The default is \code{2}.\cr}
|
|
| 26 | 26 |
|
| 27 | 27 |
\item{control_group}{(character) The level name of the group used in the denominator (where possible) when computing fold change. The default is \code{character(0)}.}
|
| 28 | 28 |
|
| 29 |
-\item{method}{(character) Fold change method. Allowed values are limited to the following: \itemize{\item{\code{"geometric"}: A log transform is applied before using group means to calculate fold change. In the non-tranformedspace this is equivalent to using geometric group means. Confidence intervals for independant and paired sampling are estimated using standard error of the mean in log transformed space before being transformed back to the original space.}\item{\code{"median"}: The group medians and the method described by Price and Bonett is used to estimate confidence intervals. For paired data standard error of the median is used to estimate confidence intervals from the median fold change of all pairs.}\item{\code{"mean"}: The group means and the method described by Price and Bonnet is used to estimate confidence intervals. For paired data standard error of the mean is used to estimate confidence intervals from the mean fold change of all pairs.}} The default is \code{"geometric"}.}
|
|
| 29 |
+\item{method}{(character) Fold change method. Allowed values are limited to the following: \itemize{ \item{\code{"geometric"}: A log transform is applied before using group means to calculate fold change. In the non-tranformedspace this is equivalent to using geometric group means. Confidence intervals for independant and paired sampling are estimated using standard error of the mean in log transformed space before being transformed back to the original space.}\item{\code{"median"}: The group medians and the method described by Price and Bonett is used to estimate confidence intervals. For paired data standard error of the median is used to estimate confidence intervals from the median fold change of all pairs.}\item{\code{"mean"}: The group means and the method described by Price and Bonnet is used to estimate confidence intervals. For paired data standard error of the mean is used to estimate confidence intervals from the mean fold change of all pairs.}} The default is \code{"geometric"}.}
|
|
| 30 | 30 |
|
| 31 |
-\item{conf_level}{(numeric) The confidence level of the interval. The default is \code{0.95}.}
|
|
| 31 |
+\item{conf_level}{(numeric) The confidence level of the interval. The default is \code{0.95}.\cr}
|
|
| 32 | 32 |
|
| 33 | 33 |
\item{...}{Additional slots and values passed to \code{struct_class}.}
|
| 34 | 34 |
} |
| ... | ... |
@@ -44,7 +44,22 @@ A \code{fold_change} object with the following \code{output} slots:
|
| 44 | 44 |
\description{
|
| 45 | 45 |
Fold change is the relative change in mean (or non-parametric equivalent) intensities of a feature between all pairs of levels in a factor. |
| 46 | 46 |
} |
| 47 |
+\section{Inheritance}{
|
|
| 48 |
+ |
|
| 49 |
+A \code{fold_change} object inherits the following \code{struct} classes: \cr\cr
|
|
| 50 |
+\code{fold_change()} ⭢ \code{model()} ⭢ \code{struct_class()}
|
|
| 51 |
+} |
|
| 52 |
+ |
|
| 47 | 53 |
\examples{
|
| 54 |
+M = fold_change( |
|
| 55 |
+ factor_name = "V1", |
|
| 56 |
+ sample_name = character(0), |
|
| 57 |
+ paired = FALSE, |
|
| 58 |
+ threshold = 2, |
|
| 59 |
+ control_group = character(0), |
|
| 60 |
+ method = "geometric", |
|
| 61 |
+ conf_level = 0.95) |
|
| 62 |
+ |
|
| 48 | 63 |
D = MTBLS79_DatasetExperiment() |
| 49 | 64 |
M = fold_change(factor_name='Class') |
| 50 | 65 |
M = model_apply(M,D) |
- remove use of square brackets as this now gets interpreted as markdown
- generate filter_by_name documentation from object, like we do for all other objects
Gavin Rhys Lloyd authored on 06/07/2023 17:19:36
| ... | ... |
@@ -26,7 +26,7 @@ fold_change( |
| 26 | 26 |
|
| 27 | 27 |
\item{control_group}{(character) The level name of the group used in the denominator (where possible) when computing fold change. The default is \code{character(0)}.}
|
| 28 | 28 |
|
| 29 |
-\item{method}{(character) Fold change method. Allowed values are limited to the following: \itemize{\item{\code{"geometric"}: A log transform is applied before using group means to calculate fold change. In the non-tranformedspace this is equivalent to using geometric group means. Confidence intervals for independant and paired sampling are estimated using standard error of the mean in log transformed space before being transformed back to the original space.}\item{\code{"median"}: The group medians and the method described by Price and Bonett\link{1} is used to estimate confidence intervals. For paired data standard error of the median is used to estimate confidence intervals from the median fold change of all pairs.}\item{\code{"mean"}: The group means and the method described by Price and Bonnet\link{1} is used to estimate confidence intervals. For paired data standard error of the mean is used to estimate confidence intervals from the mean fold change of all pairs.}} The default is \code{"geometric"}.}
|
|
| 29 |
+\item{method}{(character) Fold change method. Allowed values are limited to the following: \itemize{\item{\code{"geometric"}: A log transform is applied before using group means to calculate fold change. In the non-tranformedspace this is equivalent to using geometric group means. Confidence intervals for independant and paired sampling are estimated using standard error of the mean in log transformed space before being transformed back to the original space.}\item{\code{"median"}: The group medians and the method described by Price and Bonett is used to estimate confidence intervals. For paired data standard error of the median is used to estimate confidence intervals from the median fold change of all pairs.}\item{\code{"mean"}: The group means and the method described by Price and Bonnet is used to estimate confidence intervals. For paired data standard error of the mean is used to estimate confidence intervals from the mean fold change of all pairs.}} The default is \code{"geometric"}.}
|
|
| 30 | 30 |
|
| 31 | 31 |
\item{conf_level}{(numeric) The confidence level of the interval. The default is \code{0.95}.}
|
| 32 | 32 |
|
due to roxygen no longer needing % to be escaped.
- add markdown flag to description file
- use text format for citations (includes markdown)
- remove % from descriptions (doesnt work with current implementation)
Gavin Rhys Lloyd authored on 06/07/2023 15:19:12
| ... | ... |
@@ -26,7 +26,7 @@ fold_change( |
| 26 | 26 |
|
| 27 | 27 |
\item{control_group}{(character) The level name of the group used in the denominator (where possible) when computing fold change. The default is \code{character(0)}.}
|
| 28 | 28 |
|
| 29 |
-\item{method}{(character) Fold change method. Allowed values are limited to the following: \itemize{\item{\code{"geometric"}: A log transform is applied before using group means to calculate fold change. In the non-tranformedspace this is equivalent to using geometric group means. Confidence intervals for independant and paired sampling are estimated using standard error of the mean in log transformed space before being transformed back to the original space.}\item{\code{"median"}: The group medians and the method described by Price and Bonett[1] is used to estimate confidence intervals. For paired data standard error of the median is used to estimate confidence intervals from the median fold change of all pairs.}\item{\code{"mean"}: The group means and the method described by Price and Bonnet[1] is used to estimate confidence intervals. For paired data standard error of the mean is used to estimate confidence intervals from the mean fold change of all pairs.}} The default is \code{"geometric"}.}
|
|
| 29 |
+\item{method}{(character) Fold change method. Allowed values are limited to the following: \itemize{\item{\code{"geometric"}: A log transform is applied before using group means to calculate fold change. In the non-tranformedspace this is equivalent to using geometric group means. Confidence intervals for independant and paired sampling are estimated using standard error of the mean in log transformed space before being transformed back to the original space.}\item{\code{"median"}: The group medians and the method described by Price and Bonett\link{1} is used to estimate confidence intervals. For paired data standard error of the median is used to estimate confidence intervals from the median fold change of all pairs.}\item{\code{"mean"}: The group means and the method described by Price and Bonnet\link{1} is used to estimate confidence intervals. For paired data standard error of the mean is used to estimate confidence intervals from the mean fold change of all pairs.}} The default is \code{"geometric"}.}
|
|
| 30 | 30 |
|
| 31 | 31 |
\item{conf_level}{(numeric) The confidence level of the interval. The default is \code{0.95}.}
|
| 32 | 32 |
|
| ... | ... |
@@ -50,7 +50,7 @@ M = fold_change(factor_name='Class') |
| 50 | 50 |
M = model_apply(M,D) |
| 51 | 51 |
} |
| 52 | 52 |
\references{
|
| 53 |
-Price Jr RM, Bonett DG (2020). |
|
| 54 |
-``Confidence Intervals for Ratios of Means and Medians.'' |
|
| 55 |
-\emph{Journal of Educational and Behavioral Statistics}, \bold{45}(6), 750-770.
|
|
| 53 |
+Price Jr RM, Bonett DG (2020). "Confidence Intervals for Ratios of |
|
| 54 |
+Means and Medians." \emph{Journal of Educational and Behavioral Statistics},
|
|
| 55 |
+\emph{45}(6), 750-770.
|
|
| 56 | 56 |
} |
Gavin Rhys Lloyd authored on 26/07/2021 08:13:07
| ... | ... |
@@ -38,7 +38,7 @@ A \code{fold_change} object with the following \code{output} slots:
|
| 38 | 38 |
\code{fold_change} \tab (data.frame) The fold change between groups. \cr
|
| 39 | 39 |
\code{lower_ci} \tab (data.frame) Lower confidence interval for fold change. \cr
|
| 40 | 40 |
\code{upper_ci} \tab (data.frame) Upper confidence interval for fold change. \cr
|
| 41 |
-\code{significant} \tab (data.frame) A logical indictor of whether the fold change for a feature is greater than the threshold. \cr
|
|
| 41 |
+\code{significant} \tab (data.frame) A logical indictor of whether the calculated fold change including the estimated confidence limits is greater than the selected threshold. \cr
|
|
| 42 | 42 |
} |
| 43 | 43 |
} |
| 44 | 44 |
\description{
|
- replaces alpha with conf_level for fold change
- updates intervals for medians based on same paper used for means
- adds conf_level to ttest
Gavin Rhys Lloyd authored on 07/07/2021 15:11:50
• GitHub committed on 07/07/2021 15:11:50
| ... | ... |
@@ -5,19 +5,17 @@ |
| 5 | 5 |
\title{Fold change}
|
| 6 | 6 |
\usage{
|
| 7 | 7 |
fold_change( |
| 8 |
- alpha = 0.05, |
|
| 9 | 8 |
factor_name, |
| 10 | 9 |
paired = FALSE, |
| 11 | 10 |
sample_name = character(0), |
| 12 | 11 |
threshold = 2, |
| 13 | 12 |
control_group = character(0), |
| 14 | 13 |
method = "geometric", |
| 14 |
+ conf_level = 0.95, |
|
| 15 | 15 |
... |
| 16 | 16 |
) |
| 17 | 17 |
} |
| 18 | 18 |
\arguments{
|
| 19 |
-\item{alpha}{(numeric) The p-value cutoff for determining significance. The default is \code{0.05}.}
|
|
| 20 |
- |
|
| 21 | 19 |
\item{factor_name}{(character) The name of a sample-meta column to use.}
|
| 22 | 20 |
|
| 23 | 21 |
\item{paired}{(logical) Paired fold change. Allowed values are limited to the following: \itemize{\item{\code{"TRUE"}: Fold change is calculated taking into account paired sampling.}\item{\code{"FALSE"}: Fold change is calculated assuming there is no paired sampling.}} The default is \code{FALSE}.}
|
| ... | ... |
@@ -28,7 +26,9 @@ fold_change( |
| 28 | 26 |
|
| 29 | 27 |
\item{control_group}{(character) The level name of the group used in the denominator (where possible) when computing fold change. The default is \code{character(0)}.}
|
| 30 | 28 |
|
| 31 |
-\item{method}{(character) Fold change method. Allowed values are limited to the following: \itemize{\item{\code{"geometric"}: A log transform and a t-test is used to calculate fold change and estimate confidence intervals. In the non-transformed space this is equivalent to fold change using geometric means.}\item{\code{"median"}: A log transform and the method described by Price and Bonett to calculate fold change and estimate confidence intervals. In the non-transformed space this is equivalent to using group medians to calculate fold change.}} The default is \code{"geometric"}.}
|
|
| 29 |
+\item{method}{(character) Fold change method. Allowed values are limited to the following: \itemize{\item{\code{"geometric"}: A log transform is applied before using group means to calculate fold change. In the non-tranformedspace this is equivalent to using geometric group means. Confidence intervals for independant and paired sampling are estimated using standard error of the mean in log transformed space before being transformed back to the original space.}\item{\code{"median"}: The group medians and the method described by Price and Bonett[1] is used to estimate confidence intervals. For paired data standard error of the median is used to estimate confidence intervals from the median fold change of all pairs.}\item{\code{"mean"}: The group means and the method described by Price and Bonnet[1] is used to estimate confidence intervals. For paired data standard error of the mean is used to estimate confidence intervals from the mean fold change of all pairs.}} The default is \code{"geometric"}.}
|
|
| 30 |
+ |
|
| 31 |
+\item{conf_level}{(numeric) The confidence level of the interval. The default is \code{0.95}.}
|
|
| 32 | 32 |
|
| 33 | 33 |
\item{...}{Additional slots and values passed to \code{struct_class}.}
|
| 34 | 34 |
} |
| ... | ... |
@@ -50,7 +50,7 @@ M = fold_change(factor_name='Class') |
| 50 | 50 |
M = model_apply(M,D) |
| 51 | 51 |
} |
| 52 | 52 |
\references{
|
| 53 |
-Price RM, Bonett DG (2002). |
|
| 54 |
-``Distribution-Free Confidence Intervals for Difference and Ratio of Medians.'' |
|
| 55 |
-\emph{Journal of Statistical Computation and Simulation}, \bold{72}(2), 119-124.
|
|
| 53 |
+Price Jr RM, Bonett DG (2020). |
|
| 54 |
+``Confidence Intervals for Ratios of Means and Medians.'' |
|
| 55 |
+\emph{Journal of Educational and Behavioral Statistics}, \bold{45}(6), 750-770.
|
|
| 56 | 56 |
} |
Gavin Rhys Lloyd authored on 07/07/2021 09:37:19
• GitHub committed on 07/07/2021 09:37:19
| ... | ... |
@@ -33,7 +33,13 @@ fold_change( |
| 33 | 33 |
\item{...}{Additional slots and values passed to \code{struct_class}.}
|
| 34 | 34 |
} |
| 35 | 35 |
\value{
|
| 36 |
-A \code{fold_change} object.
|
|
| 36 |
+A \code{fold_change} object with the following \code{output} slots:
|
|
| 37 |
+\tabular{ll}{
|
|
| 38 |
+\code{fold_change} \tab (data.frame) The fold change between groups. \cr
|
|
| 39 |
+\code{lower_ci} \tab (data.frame) Lower confidence interval for fold change. \cr
|
|
| 40 |
+\code{upper_ci} \tab (data.frame) Upper confidence interval for fold change. \cr
|
|
| 41 |
+\code{significant} \tab (data.frame) A logical indictor of whether the fold change for a feature is greater than the threshold. \cr
|
|
| 42 |
+} |
|
| 37 | 43 |
} |
| 38 | 44 |
\description{
|
| 39 | 45 |
Fold change is the relative change in mean (or non-parametric equivalent) intensities of a feature between all pairs of levels in a factor. |
occurred due to capitalisation of some column names in sample meta of MTBLS79 in pmp
Gavin Rhys Lloyd authored on 26/04/2021 15:00:13
| ... | ... |
@@ -40,7 +40,7 @@ Fold change is the relative change in mean (or non-parametric equivalent) intens |
| 40 | 40 |
} |
| 41 | 41 |
\examples{
|
| 42 | 42 |
D = MTBLS79_DatasetExperiment() |
| 43 |
-M = fold_change(factor_name='class') |
|
| 43 |
+M = fold_change(factor_name='Class') |
|
| 44 | 44 |
M = model_apply(M,D) |
| 45 | 45 |
} |
| 46 | 46 |
\references{
|
* 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
| ... | ... |
@@ -2,7 +2,7 @@ |
| 2 | 2 |
% Please edit documentation in R/fold_change_class.R |
| 3 | 3 |
\name{fold_change}
|
| 4 | 4 |
\alias{fold_change}
|
| 5 |
-\title{fold change class}
|
|
| 5 |
+\title{Fold change}
|
|
| 6 | 6 |
\usage{
|
| 7 | 7 |
fold_change( |
| 8 | 8 |
alpha = 0.05, |
| ... | ... |
@@ -11,35 +11,40 @@ fold_change( |
| 11 | 11 |
sample_name = character(0), |
| 12 | 12 |
threshold = 2, |
| 13 | 13 |
control_group = character(0), |
| 14 |
+ method = "geometric", |
|
| 14 | 15 |
... |
| 15 | 16 |
) |
| 16 | 17 |
} |
| 17 | 18 |
\arguments{
|
| 18 |
-\item{alpha}{confidence level to use for intervals}
|
|
| 19 |
+\item{alpha}{(numeric) The p-value cutoff for determining significance. The default is \code{0.05}.}
|
|
| 19 | 20 |
|
| 20 |
-\item{factor_name}{the sample_meta column to use}
|
|
| 21 |
+\item{factor_name}{(character) The name of a sample-meta column to use.}
|
|
| 21 | 22 |
|
| 22 |
-\item{paired}{TRUE or [FALSE] to account for paired samples}
|
|
| 23 |
+\item{paired}{(logical) Paired fold change. Allowed values are limited to the following: \itemize{\item{\code{"TRUE"}: Fold change is calculated taking into account paired sampling.}\item{\code{"FALSE"}: Fold change is calculated assuming there is no paired sampling.}} The default is \code{FALSE}.}
|
|
| 23 | 24 |
|
| 24 |
-\item{sample_name}{the sample_meta column name to use for a paired samples}
|
|
| 25 |
+\item{sample_name}{(character) The name of a sample_meta column containing sample identifiers for paired sampling. The default is \code{character(0)}.}
|
|
| 25 | 26 |
|
| 26 |
-\item{threshold}{a threshold to define fold change as 'significant'.}
|
|
| 27 |
+\item{threshold}{(numeric) The fold change threshold for labelling features as significant. The default is \code{2}.}
|
|
| 27 | 28 |
|
| 28 |
-\item{control_group}{a level of factor name to use as the control group for
|
|
| 29 |
-calculations.} |
|
| 29 |
+\item{control_group}{(character) The level name of the group used in the denominator (where possible) when computing fold change. The default is \code{character(0)}.}
|
|
| 30 | 30 |
|
| 31 |
-\item{...}{additional slots and values passed to struct_class}
|
|
| 31 |
+\item{method}{(character) Fold change method. Allowed values are limited to the following: \itemize{\item{\code{"geometric"}: A log transform and a t-test is used to calculate fold change and estimate confidence intervals. In the non-transformed space this is equivalent to fold change using geometric means.}\item{\code{"median"}: A log transform and the method described by Price and Bonett to calculate fold change and estimate confidence intervals. In the non-transformed space this is equivalent to using group medians to calculate fold change.}} The default is \code{"geometric"}.}
|
|
| 32 |
+ |
|
| 33 |
+\item{...}{Additional slots and values passed to \code{struct_class}.}
|
|
| 32 | 34 |
} |
| 33 | 35 |
\value{
|
| 34 |
-struct object |
|
| 36 |
+A \code{fold_change} object.
|
|
| 35 | 37 |
} |
| 36 | 38 |
\description{
|
| 37 |
-Calculates fold change between groups for all features in a DatasetExperiment, based on |
|
| 38 |
-a log transform and t-test. |
|
| 39 |
+Fold change is the relative change in mean (or non-parametric equivalent) intensities of a feature between all pairs of levels in a factor. |
|
| 39 | 40 |
} |
| 40 | 41 |
\examples{
|
| 41 | 42 |
D = MTBLS79_DatasetExperiment() |
| 42 | 43 |
M = fold_change(factor_name='class') |
| 43 | 44 |
M = model_apply(M,D) |
| 44 |
- |
|
| 45 |
+} |
|
| 46 |
+\references{
|
|
| 47 |
+Price RM, Bonett DG (2002). |
|
| 48 |
+``Distribution-Free Confidence Intervals for Difference and Ratio of Medians.'' |
|
| 49 |
+\emph{Journal of Statistical Computation and Simulation}, \bold{72}(2), 119-124.
|
|
| 45 | 50 |
} |
Gavin Rhys Lloyd authored on 11/02/2020 13:19:28
| ... | ... |
@@ -38,7 +38,7 @@ Calculates fold change between groups for all features in a DatasetExperiment, b |
| 38 | 38 |
a log transform and t-test. |
| 39 | 39 |
} |
| 40 | 40 |
\examples{
|
| 41 |
-D = sbcms_DatasetExperiment() |
|
| 41 |
+D = MTBLS79_DatasetExperiment() |
|
| 42 | 42 |
M = fold_change(factor_name='class') |
| 43 | 43 |
M = model_apply(M,D) |
| 44 | 44 |
|
Gavin Rhys Lloyd authored on 07/02/2020 17:02:22
Gavin Rhys Lloyd authored on 04/02/2020 17:18:11
| ... | ... |
@@ -4,10 +4,31 @@ |
| 4 | 4 |
\alias{fold_change}
|
| 5 | 5 |
\title{fold change class}
|
| 6 | 6 |
\usage{
|
| 7 |
-fold_change(...) |
|
| 7 |
+fold_change( |
|
| 8 |
+ alpha = 0.05, |
|
| 9 |
+ factor_name, |
|
| 10 |
+ paired = FALSE, |
|
| 11 |
+ sample_name = character(0), |
|
| 12 |
+ threshold = 2, |
|
| 13 |
+ control_group, |
|
| 14 |
+ ... |
|
| 15 |
+) |
|
| 8 | 16 |
} |
| 9 | 17 |
\arguments{
|
| 10 |
-\item{...}{slots and values for the new object}
|
|
| 18 |
+\item{alpha}{confidence level to use for intervals}
|
|
| 19 |
+ |
|
| 20 |
+\item{factor_name}{the sample_meta column to use}
|
|
| 21 |
+ |
|
| 22 |
+\item{paired}{TRUE or [FALSE] to account for paired samples}
|
|
| 23 |
+ |
|
| 24 |
+\item{sample_name}{the sample_meta column name to use for a paired samples}
|
|
| 25 |
+ |
|
| 26 |
+\item{threshold}{a threshold to define fold change as 'significant'.}
|
|
| 27 |
+ |
|
| 28 |
+\item{control_group}{a level of factor name to use as the control group for
|
|
| 29 |
+calculations.} |
|
| 30 |
+ |
|
| 31 |
+\item{...}{additional slots and values passed to struct_class}
|
|
| 11 | 32 |
} |
| 12 | 33 |
\value{
|
| 13 | 34 |
struct object |
| ... | ... |
@@ -16,23 +37,6 @@ struct object |
| 16 | 37 |
Calculates fold change between groups for all features in a DatasetExperiment, based on |
| 17 | 38 |
a log transform and t-test. |
| 18 | 39 |
} |
| 19 |
-\section{Slots}{
|
|
| 20 |
- |
|
| 21 |
-\describe{
|
|
| 22 |
-\item{\code{alpha}}{confidence level to use for intervals}
|
|
| 23 |
- |
|
| 24 |
-\item{\code{factor_name}}{the sample_meta column to use}
|
|
| 25 |
- |
|
| 26 |
-\item{\code{paired}}{TRUE or [FALSE] to account for paired samples}
|
|
| 27 |
- |
|
| 28 |
-\item{\code{sample_name}}{the sample_meta column name to use for a paired samples}
|
|
| 29 |
- |
|
| 30 |
-\item{\code{threshold}}{a threshold to define fold change as 'significant'.}
|
|
| 31 |
- |
|
| 32 |
-\item{\code{control_group}}{a level of factor name to use as the control group for
|
|
| 33 |
-calculations.} |
|
| 34 |
-}} |
|
| 35 |
- |
|
| 36 | 40 |
\examples{
|
| 37 | 41 |
D = sbcms_DatasetExperiment() |
| 38 | 42 |
M = fold_change(factor_name='class') |
Gavin Rhys Lloyd authored on 19/12/2019 15:14:02
| ... | ... |
@@ -9,6 +9,9 @@ fold_change(...) |
| 9 | 9 |
\arguments{
|
| 10 | 10 |
\item{...}{slots and values for the new object}
|
| 11 | 11 |
} |
| 12 |
+\value{
|
|
| 13 |
+struct object |
|
| 14 |
+} |
|
| 12 | 15 |
\description{
|
| 13 | 16 |
Calculates fold change between groups for all features in a DatasetExperiment, based on |
| 14 | 17 |
a log transform and t-test. |
...update some documentation
Gavin Rhys Lloyd authored on 17/12/2019 17:24:38
| ... | ... |
@@ -7,23 +7,29 @@ |
| 7 | 7 |
fold_change(...) |
| 8 | 8 |
} |
| 9 | 9 |
\arguments{
|
| 10 |
-\item{alpha}{confidence level to use for intervals}
|
|
| 10 |
+\item{...}{slots and values for the new object}
|
|
| 11 |
+} |
|
| 12 |
+\description{
|
|
| 13 |
+Calculates fold change between groups for all features in a DatasetExperiment, based on |
|
| 14 |
+a log transform and t-test. |
|
| 15 |
+} |
|
| 16 |
+\section{Slots}{
|
|
| 17 |
+ |
|
| 18 |
+\describe{
|
|
| 19 |
+\item{\code{alpha}}{confidence level to use for intervals}
|
|
| 11 | 20 |
|
| 12 |
-\item{factor_name}{the sample_meta column to use}
|
|
| 21 |
+\item{\code{factor_name}}{the sample_meta column to use}
|
|
| 13 | 22 |
|
| 14 |
-\item{paired}{TRUE or [FALSE] to account for paired samples}
|
|
| 23 |
+\item{\code{paired}}{TRUE or [FALSE] to account for paired samples}
|
|
| 15 | 24 |
|
| 16 |
-\item{sample_name}{the sample_meta column name to use for a paired samples}
|
|
| 25 |
+\item{\code{sample_name}}{the sample_meta column name to use for a paired samples}
|
|
| 17 | 26 |
|
| 18 |
-\item{threshold}{a threshold to define fold change as 'significant'.}
|
|
| 27 |
+\item{\code{threshold}}{a threshold to define fold change as 'significant'.}
|
|
| 19 | 28 |
|
| 20 |
-\item{control_group}{a level of factor name to use as the control group for
|
|
| 29 |
+\item{\code{control_group}}{a level of factor name to use as the control group for
|
|
| 21 | 30 |
calculations.} |
| 22 |
-} |
|
| 23 |
-\description{
|
|
| 24 |
-Calculates fold change between groups for all features in a DatasetExperiment, based on |
|
| 25 |
-a log transform and t-test. |
|
| 26 |
-} |
|
| 31 |
+}} |
|
| 32 |
+ |
|
| 27 | 33 |
\examples{
|
| 28 | 34 |
D = sbcms_DatasetExperiment() |
| 29 | 35 |
M = fold_change(factor_name='class') |
...rename all function with dot to underscore
replace dataset with DatasetExperiment
Gavin Rhys Lloyd authored on 17/12/2019 15:48:01
| 1 | 1 |
new file mode 100644 |
| ... | ... |
@@ -0,0 +1,32 @@ |
| 1 |
+% Generated by roxygen2: do not edit by hand |
|
| 2 |
+% Please edit documentation in R/fold_change_class.R |
|
| 3 |
+\name{fold_change}
|
|
| 4 |
+\alias{fold_change}
|
|
| 5 |
+\title{fold change class}
|
|
| 6 |
+\usage{
|
|
| 7 |
+fold_change(...) |
|
| 8 |
+} |
|
| 9 |
+\arguments{
|
|
| 10 |
+\item{alpha}{confidence level to use for intervals}
|
|
| 11 |
+ |
|
| 12 |
+\item{factor_name}{the sample_meta column to use}
|
|
| 13 |
+ |
|
| 14 |
+\item{paired}{TRUE or [FALSE] to account for paired samples}
|
|
| 15 |
+ |
|
| 16 |
+\item{sample_name}{the sample_meta column name to use for a paired samples}
|
|
| 17 |
+ |
|
| 18 |
+\item{threshold}{a threshold to define fold change as 'significant'.}
|
|
| 19 |
+ |
|
| 20 |
+\item{control_group}{a level of factor name to use as the control group for
|
|
| 21 |
+calculations.} |
|
| 22 |
+} |
|
| 23 |
+\description{
|
|
| 24 |
+Calculates fold change between groups for all features in a DatasetExperiment, based on |
|
| 25 |
+a log transform and t-test. |
|
| 26 |
+} |
|
| 27 |
+\examples{
|
|
| 28 |
+D = sbcms_DatasetExperiment() |
|
| 29 |
+M = fold_change(factor_name='class') |
|
| 30 |
+M = model_apply(M,D) |
|
| 31 |
+ |
|
| 32 |
+} |