diff --git a/docs/articles/metabolyseR.html b/docs/articles/metabolyseR.html index 8a7bcd21..06f10b39 100644 --- a/docs/articles/metabolyseR.html +++ b/docs/articles/metabolyseR.html @@ -644,7 +644,7 @@ 

 analysis <- metabolyse(abr1$neg[,1:200],abr1$fact,p) 
## 
-## metabolyseR  v0.14.4 Sun Nov  7 22:26:41 2021
+## metabolyseR v0.14.4 Sun Nov 7 22:47:35 2021 
## ________________________________________________________________________________
## Parameters:
 ## pre-treatment
@@ -668,13 +668,13 @@ 

 
## ________________________________________________________________________________

 
## Pre-treatment …
 
-Pre-treatment   ✓ [0.8S]
+Pre-treatment   ✓ [0.9S]
 ## Modelling …
 
-Modelling   ✓ [3.3S]
+Modelling   ✓ [3.7S]
 ## ________________________________________________________________________________
 ## 
-## Complete! [4S]

+## Complete! [4.6S]

Note: If a data pre-treatment step is not performed prior to modelling or correlation analysis, the raw data will automatically be used.

The analysis object containing the analysis results can be printed to provide some basic information about the results of the analysis.

@@ -682,19 +682,19 @@ 

 
## 
 ## metabolyseR v0.14.4
 ## Analysis:
-##  Sun Nov  7 22:26:41 2021
+##  Sun Nov  7 22:47:35 2021
 ## 
 ##  Raw Data:
 ##      No. samples = 120
 ##      No. features = 200
 ## 
 ##  Pre-treated Data:
-##      Sun Nov  7 22:26:42 2021
+##      Sun Nov  7 22:47:35 2021
 ##      No. samples = 120
 ##      No. features = 48
 ## 
 ##  Modelling:
-##      Sun Nov  7 22:26:45 2021
+##      Sun Nov  7 22:47:39 2021
 ##      Methods: randomForest
@@ -709,7 +709,7 @@ 

 analysis <- reAnalyse(analysis,parameters)
## 
-## metabolyseR v0.14.4 Sun Nov  7 22:26:45 2021
+## metabolyseR v0.14.4 Sun Nov  7 22:47:39 2021
 ## ________________________________________________________________________________
 ## Parameters:
 ## correlations
@@ -729,23 +729,23 @@ 

 
## 
 ## metabolyseR v0.14.4
 ## Analysis:
-##  Sun Nov  7 22:26:41 2021
+##  Sun Nov  7 22:47:35 2021
 ## 
 ##  Raw Data:
 ##      No. samples = 120
 ##      No. features = 200
 ## 
 ##  Pre-treated Data:
-##      Sun Nov  7 22:26:42 2021
+##      Sun Nov  7 22:47:35 2021
 ##      No. samples = 120
 ##      No. features = 48
 ## 
 ##  Modelling:
-##      Sun Nov  7 22:26:45 2021
+##      Sun Nov  7 22:47:39 2021
 ##      Methods: randomForest
 ## 
 ##  Correlations:
-##      Sun Nov  7 22:26:45 2021
+##      Sun Nov  7 22:47:40 2021
 ##      No. correlations = 140

diff --git a/docs/articles/modelling.html b/docs/articles/modelling.html index a4c7793c..6351bf92 100644 --- a/docs/articles/modelling.html +++ b/docs/articles/modelling.html @@ -737,7 +737,7 @@

The analysis can then be executed.

analysis <- metabolyse(abr1$neg,abr1$fact,p)
 #> 
-#> metabolyseR  v0.14.4 Sun Nov  7 22:27:51 2021
+#> metabolyseR  v0.14.4 Sun Nov  7 22:48:55 2021
 #> ________________________________________________________________________________
 #> Parameters:
 #> pre-treatment
@@ -770,13 +770,13 @@ 

 #> ________________________________________________________________________________
 #> Pre-treatment …
 
-Pre-treatment   ✓ [6.2S]
+Pre-treatment   ✓ [7.3S]
 #> Modelling …
 
-Modelling   ✓ [4.3S]
+Modelling   ✓ [5.2S]
 #> ________________________________________________________________________________
 #> 
-#> Complete! [10.5S]
+#> Complete! [12.5S]

The results for the modelling can be specifically extracted using the following.

 analysisResults(analysis,'modelling')
diff --git a/docs/articles/modelling_files/figure-html/outlier-detect-1.png b/docs/articles/modelling_files/figure-html/outlier-detect-1.png
index 7e6fe57b..e87731cc 100644
Binary files a/docs/articles/modelling_files/figure-html/outlier-detect-1.png and b/docs/articles/modelling_files/figure-html/outlier-detect-1.png differ
diff --git a/docs/articles/modelling_files/figure-html/regression-mds-1.png b/docs/articles/modelling_files/figure-html/regression-mds-1.png
index d74eec99..13f34136 100644
Binary files a/docs/articles/modelling_files/figure-html/regression-mds-1.png and b/docs/articles/modelling_files/figure-html/regression-mds-1.png differ
diff --git a/docs/articles/pre_treatment.html b/docs/articles/pre_treatment.html
index 567d17a9..3652b1fe 100644
--- a/docs/articles/pre_treatment.html
+++ b/docs/articles/pre_treatment.html
@@ -500,7 +500,7 @@ 

 
The pre-treatment routine can then be executed.

 
analysis <- metabolyse(abr1$neg,abr1$fact,p)
 #> 
-#> metabolyseR  v0.14.4 Sun Nov  7 22:31:41 2021
+#> metabolyseR  v0.14.4 Sun Nov  7 22:53:23 2021
 #> ________________________________________________________________________________
 #> Parameters:
 #> pre-treatment
@@ -517,24 +517,24 @@ 

 #> ________________________________________________________________________________
 #> Pre-treatment …
 
-Pre-treatment   ✓ [9.1S]
+Pre-treatment   ✓ [8.6S]
 #> ________________________________________________________________________________
 #> 
-#> Complete! [9.1S]

+#> Complete! [8.6S]

Printing the analysis object shows the resulting data from the pre-treatment routine.

 print(analysis)
 #> 
 #> metabolyseR v0.14.4
 #> Analysis:
-#>  Sun Nov  7 22:31:41 2021
+#>  Sun Nov  7 22:53:23 2021
 #> 
 #>  Raw Data:
 #>      No. samples = 120
 #>      No. features = 2000
 #> 
 #>  Pre-treated Data:
-#>      Sun Nov  7 22:31:50 2021
+#>      Sun Nov  7 22:53:31 2021
 #>      No. samples = 60
 #>      No. features = 1723

The pre-treated data can be extracted from the Analysis object using several methods.

diff --git a/docs/index.html b/docs/index.html index 103c9215..07865a44 100644 --- a/docs/index.html +++ b/docs/index.html @@ -185,18 +185,18 @@ 

 explan_feat
 #> # A tibble: 379 × 10
-#>    Response Comparison  Feature term        df   sumsq  meansq statistic  p.value
-#>    <chr>    <chr>       <chr>   <chr>    <dbl>   <dbl>   <dbl>     <dbl>    <dbl>
-#>  1 day      1~2~3~4~5~H N341    response     5 3.88e-4 7.76e-5     137.  1.55e-46
-#>  2 day      1~2~3~4~5~H N133    response     5 7.00e-5 1.40e-5     126.  8.63e-45
-#>  3 day      1~2~3~4~5~H N163    response     5 6.01e-5 1.20e-5     117.  2.95e-43
-#>  4 day      1~2~3~4~5~H N1087   response     5 2.42e-6 4.84e-7      99.8 5.61e-40
-#>  5 day      1~2~3~4~5~H N171    response     5 2.25e-7 4.50e-8      95.7 3.84e-39
-#>  6 day      1~2~3~4~5~H N513    response     5 3.38e-6 6.76e-7      95.3 4.78e-39
-#>  7 day      1~2~3~4~5~H N1025   response     5 2.78e-6 5.56e-7      91.0 3.91e-38
-#>  8 day      1~2~3~4~5~H N342    response     5 3.71e-6 7.41e-7      90.3 5.32e-38
-#>  9 day      1~2~3~4~5~H N1083   response     5 5.11e-5 1.02e-5      89.0 1.06e-37
-#> 10 day      1~2~3~4~5~H N1085   response     5 1.10e-5 2.19e-6      83.4 1.92e-36
+#>    Response Comparison  Feature term      df    sumsq  meansq statistic  p.value
+#>    <chr>    <chr>       <chr>   <chr>  <dbl>    <dbl>   <dbl>     <dbl>    <dbl>
+#>  1 day      1~2~3~4~5~H N341    respo…     5  3.88e-4 7.76e-5     137.  1.55e-46
+#>  2 day      1~2~3~4~5~H N133    respo…     5  7.00e-5 1.40e-5     126.  8.63e-45
+#>  3 day      1~2~3~4~5~H N163    respo…     5  6.01e-5 1.20e-5     117.  2.95e-43
+#>  4 day      1~2~3~4~5~H N1087   respo…     5  2.42e-6 4.84e-7      99.8 5.61e-40
+#>  5 day      1~2~3~4~5~H N171    respo…     5  2.25e-7 4.50e-8      95.7 3.84e-39
+#>  6 day      1~2~3~4~5~H N513    respo…     5  3.38e-6 6.76e-7      95.3 4.78e-39
+#>  7 day      1~2~3~4~5~H N1025   respo…     5  2.78e-6 5.56e-7      91.0 3.91e-38
+#>  8 day      1~2~3~4~5~H N342    respo…     5  3.71e-6 7.41e-7      90.3 5.32e-38
+#>  9 day      1~2~3~4~5~H N1083   respo…     5  5.11e-5 1.02e-5      89.0 1.06e-37
+#> 10 day      1~2~3~4~5~H N1085   respo…     5  1.10e-5 2.19e-6      83.4 1.92e-36
 #> # … with 369 more rows, and 1 more variable: adjusted.p.value <dbl>

The ANOVA has identified 379 features significantly explanatory over the infection time course. A heat map of the mean relative intensity for each class of these explanatory features can be plotted to visualise their trends between the infection time point classes.

@@ -244,6 +244,7 @@ 
Dev status

 
  • codecov
    • 
 
  • license
    • 
 
  • DOI
    • 
+
  • GitHub release
    •
    diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 5b375c93..b6546ce4 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -6,7 +6,7 @@ articles: modelling: modelling.html pre_treatment: pre_treatment.html quick_start: quick_start.html -last_built: 2021-11-07T22:25Z +last_built: 2021-11-07T22:46Z urls: reference: https://jasenfinch.github.io/metabolyseR//reference article: https://jasenfinch.github.io/metabolyseR//articles diff --git a/docs/reference/metabolyse.html b/docs/reference/metabolyse.html index 9a2f996b..f355247c 100644 --- a/docs/reference/metabolyse.html +++ b/docs/reference/metabolyse.html @@ -205,7 +205,7 @@

    Examp abr1$fact, p) #> -#> metabolyseR v0.14.4 Sun Nov 7 22:25:45 2021 +#> metabolyseR v0.14.4 Sun Nov 7 22:46:34 2021 #> ________________________________________________________________________________ #> Parameters: #> pre-treatment @@ -226,16 +226,16 @@

    Examp #> Pre-treatment … #> Pre-treatment ✓ [0.8S] #> Modelling … -#> Modelling ✓ [0.5S] +#> Modelling ✓ [0.6S] #> ________________________________________________________________________________ #> -#> Complete! [1.3S] +#> Complete! [1.4S] ## Re-analyse to include correlation analysis analysis <- reAnalyse(analysis, parameters = analysisParameters('correlations')) #> -#> metabolyseR v0.14.4 Sun Nov 7 22:25:47 2021 +#> metabolyseR v0.14.4 Sun Nov 7 22:46:35 2021 #> ________________________________________________________________________________ #> Parameters: #> correlations @@ -255,23 +255,23 @@

    Examp #> #> metabolyseR v0.14.4 #> Analysis: -#> Sun Nov 7 22:25:45 2021 +#> Sun Nov 7 22:46:34 2021 #> #> Raw Data: #> No. samples = 120 #> No. features = 200 #> #> Pre-treated Data: -#> Sun Nov 7 22:25:46 2021 +#> Sun Nov 7 22:46:34 2021 #> No. samples = 120 #> No. features = 48 #> #> Modelling: -#> Sun Nov 7 22:25:47 2021 +#> Sun Nov 7 22:46:35 2021 #> Methods: anova #> #> Correlations: -#> Sun Nov 7 22:25:47 2021 +#> Sun Nov 7 22:46:35 2021 #> No. correlations = 140