Bioconductor Code: structToolbox

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update to new ontology system (#63)

Gavin Rhys Lloyd authored on 26/07/2021 09:30:25 • GitHub committed on 26/07/2021 09:30:25
Showing 1 changed files

@@ -13,7 +13,7 @@ log_transform = function(base=10,...) {
                                      .log_transform<-setClass(
                                          "log_transform",
                                     -    contains = c('model','stato'),
                                     +    contains = c('model'),
                                          slots=c(base='entity',
                                              transformed='entity'
                                          ),
@@ -24,7 +24,7 @@ log_transform = function(base=10,...) {
                                              predicted = 'transformed',
                                              .params=c('base'),
                                              .outputs=c('transformed'),
                                     -        stato_id = 'OBI:0200094',
                                     +        ontology = 'OBI:0200094',
                                              base=entity(name = 'Logarithm base',
                                                  description = 'The base of the logarithm used for the transform.',
                                                  value = 10,

Browse code

Release 3 12 candidate (#32)

* 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
Showing 1 changed files

@@ -1,15 +1,11 @@
                                     -#' log transform
                                     -#'
                                     -#' Applies a log transform to the input data
                                     -#' @param base The base of the logarithm. Default is 10, resulting in a log10 transformation of the data.
                                     -#' @param ... additional slots and values passed to struct_class
                                     +#' @eval get_description('log_transform')
                                      #' @return struct object
                                      #' @export log_transform
                                      #' @examples
                                      #' M = log_transform()
                                      log_transform = function(base=10,...) {
                                          out=struct::new_struct('log_transform',
                                     -        base=10,
                                     +        base=base,
                                              ...)
                                          return(out)
+                                     }
@@ -17,24 +13,24 @@ log_transform = function(base=10,...) {
                                      .log_transform<-setClass(
                                          "log_transform",
                                     -    contains = c('model'),
                                     +    contains = c('model','stato'),
                                          slots=c(base='entity',
                                              transformed='entity'
                                          ),
                                          prototype=list(name = 'logarithm transform',
                                     -        description = 'applies a log tranform to the data.',
                                     +        description = 'A logarithmic transform is applied to all values in the data matrix.',
                                              type = 'transform',
                                              predicted = 'transformed',
                                              .params=c('base'),
                                              .outputs=c('transformed'),
+                                    -
                                     -        base=entity(name = 'logarithm base',
                                     -            description = 'The base of the logarithm used for the tranform.',
                                     +        stato_id = 'OBI:0200094',
                                     +        base=entity(name = 'Logarithm base',
                                     +            description = 'The base of the logarithm used for the transform.',
                                                  value = 10,
                                                  type='numeric'),
                                     -        transformed=entity(name = 'log transformed DatasetExperiment',
                                     +        transformed=entity(name = 'Log transformed DatasetExperiment',
                                                  description = 'A DatasetExperiment object containing the log transformed data.',
                                                  type='DatasetExperiment',
                                                  value=DatasetExperiment()

@@ -1,6 +1,7 @@
                                      #' log transform
                                      #'
                                      #' applies a log transform to the input data
                                     +#' @param ... slots and values for the new object
                                      #' @export log_transform
                                      #' @examples
                                      #' M = log_transform()
@@ -36,6 +37,7 @@ log_transform = function(...) {
+                                         )
+                                     )
                                     +#' @param ... slots and values for the new object
                                      #' @export
                                      #' @template model_apply
                                      setMethod(f="model_apply",

@@ -30,7 +30,7 @@ log_transform<-setClass(
+                                     )
                                      #' @export
                                     -#' @template method_apply
                                     +#' @template model_apply
                                      setMethod(f="model.apply",
                                          signature=c("log_transform","dataset"),
                                          definition=function(M,D)

                                     new file mode 100644
@@ -0,0 +1,49 @@
                                     +#' log transform
                                     +#'
                                     +#' applies a log transform to the input data
                                     +#' @export log_transform
                                     +log_transform<-setClass(
                                     +  "log_transform",
                                     +  contains = c('method'),
                                     +  slots=c(params.base='entity',
                                     +          outputs.transformed='entity'
                                     +  ),
+                                    +
                                     +  prototype=list(name = 'logarithm transform',
                                     +                 description = 'applies a log tranform to the data.',
                                     +                 type = 'transform',
                                     +                 predicted = 'transformed',
                                     +                 params=c('base'),
                                     +                 outputs=c('transformed'),
+                                    +
                                     +                 params.qc_label=entity(name = 'logarithm base',
                                     +                                        description = 'The base of the logarithm used for the tranform.',
                                     +                                        value = 10,
                                     +                                        type='numeric'),
+                                    +
                                     +                 outputs.transformed=entity(name = 'log transformed dataset',
                                     +                                            description = 'A dataset object containing the log transformed data.',
                                     +                                            type='dataset',
                                     +                                            value=dataset()
                                     +                 )
                                     +  )
                                     +)
+                                    +
                                     +#' @export
                                     +setMethod(f="method.apply",
                                     +          signature=c("log_transform","dataset"),
                                     +          definition=function(M,D)
                                     +          {
                                     +            opt=param.list(M)
+                                    +
                                     +            smeta=dataset.sample_meta(D)
                                     +            x=dataset.data(D)
+                                    +
                                     +            out = log(x,base = opt$base)
                                     +            dataset.data(D) = as.data.frame(out)
+                                    +
                                     +            output.value(M,'transformed') = D
+                                    +
                                     +            return(M)
                                     +          }
                                     +)

update to new ontology system (#63)

Release 3 12 candidate (#32)

update to use new struct class constructors

incremental changes to use struct class constructors

remove all params_ and outputs_ tags

add @return to documentation

fix broken tests and...

use class contructors and...

change to use train/predict and apply

convert all methods to models

use method_apply roxygen template

update documentation and minor bioccheck fixes

change indentation for biocCheck

fix incorrect slot name for log_transform

remove params and outputs slots

initial commit