diff --git a/apple-touch-icon-120x120.png b/apple-touch-icon-120x120.png index 9e59f9e0..03117310 100644 Binary files a/apple-touch-icon-120x120.png and b/apple-touch-icon-120x120.png differ diff --git a/apple-touch-icon-152x152.png b/apple-touch-icon-152x152.png index 03e8ed3d..33bbfb42 100644 Binary files a/apple-touch-icon-152x152.png and b/apple-touch-icon-152x152.png differ diff --git a/apple-touch-icon-180x180.png b/apple-touch-icon-180x180.png index 785839f2..9f334268 100644 Binary files a/apple-touch-icon-180x180.png and b/apple-touch-icon-180x180.png differ diff --git a/apple-touch-icon-60x60.png b/apple-touch-icon-60x60.png index 31a20636..e65c5f98 100644 Binary files a/apple-touch-icon-60x60.png and b/apple-touch-icon-60x60.png differ diff --git a/apple-touch-icon-76x76.png b/apple-touch-icon-76x76.png index e33185ee..915dbf57 100644 Binary files a/apple-touch-icon-76x76.png and b/apple-touch-icon-76x76.png differ diff --git a/apple-touch-icon.png b/apple-touch-icon.png index 775ed914..3c037692 100644 Binary files a/apple-touch-icon.png and b/apple-touch-icon.png differ diff --git a/favicon-16x16.png b/favicon-16x16.png index 29134f44..46096e56 100644 Binary files a/favicon-16x16.png and b/favicon-16x16.png differ diff --git a/favicon-32x32.png b/favicon-32x32.png index b1796375..52460c40 100644 Binary files a/favicon-32x32.png and b/favicon-32x32.png differ diff --git a/index.html b/index.html index 4e337b93..b28bba2a 100644 --- a/index.html +++ b/index.html @@ -531,18 +531,18 @@

Reduce dimensions pivot_sample() |> select(contains("tSNE"), everything()) 
## [90m# A tibble: 251 × 4[39m
-##     tSNE1   tSNE2 .sample                      Call 
-##     [3m[90m<dbl>[39m[23m   [3m[90m<dbl>[39m[23m [3m[90m<chr>[39m[23m                        [3m[90m<fct>[39m[23m
-## [90m 1[39m -[31m12[39m[31m.[39m[31m7[39m    0.987 TCGA-A1-A0SD-01A-11R-A115-07 LumA 
-## [90m 2[39m   4.36   6.17  TCGA-A1-A0SF-01A-11R-A144-07 LumA 
-## [90m 3[39m -[31m17[39m[31m.[39m[31m0[39m    2.40  TCGA-A1-A0SG-01A-11R-A144-07 LumA 
-## [90m 4[39m  -[31m5[39m[31m.[39m[31m84[39m   5.08  TCGA-A1-A0SH-01A-11R-A084-07 LumA 
-## [90m 5[39m  -[31m9[39m[31m.[39m[31m39[39m   4.68  TCGA-A1-A0SI-01A-11R-A144-07 LumB 
-## [90m 6[39m   5.81  -[31m2[39m[31m.[39m[31m71[39m  TCGA-A1-A0SJ-01A-11R-A084-07 LumA 
-## [90m 7[39m  32.1    9.09  TCGA-A1-A0SK-01A-12R-A084-07 Basal
-## [90m 8[39m   4.47  -[31m9[39m[31m.[39m[31m44[39m  TCGA-A1-A0SM-01A-11R-A084-07 LumA 
-## [90m 9[39m   4.95 -[31m10[39m[31m.[39m[31m9[39m   TCGA-A1-A0SN-01A-11R-A144-07 LumB 
-## [90m10[39m -[31m25[39m[31m.[39m[31m6[39m   -[31m3[39m[31m.[39m[31m70[39m  TCGA-A1-A0SQ-01A-21R-A144-07 LumA 
+##     tSNE1  tSNE2 .sample                      Call 
+##     [3m[90m<dbl>[39m[23m  [3m[90m<dbl>[39m[23m [3m[90m<chr>[39m[23m                        [3m[90m<fct>[39m[23m
+## [90m 1[39m  -[31m2[39m[31m.[39m[31m64[39m   9.66 TCGA-A1-A0SD-01A-11R-A115-07 LumA 
+## [90m 2[39m  -[31m1[39m[31m.[39m[31m57[39m  -[31m2[39m[31m.[39m[31m45[39m TCGA-A1-A0SF-01A-11R-A144-07 LumA 
+## [90m 3[39m  -[31m3[39m[31m.[39m[31m13[39m  16.9  TCGA-A1-A0SG-01A-11R-A144-07 LumA 
+## [90m 4[39m  10.7    1.92 TCGA-A1-A0SH-01A-11R-A084-07 LumA 
+## [90m 5[39m  -[31m1[39m[31m.[39m[31m78[39m   5.61 TCGA-A1-A0SI-01A-11R-A144-07 LumB 
+## [90m 6[39m  -[31m7[39m[31m.[39m[31m48[39m  -[31m6[39m[31m.[39m[31m0[39m[31m2[39m TCGA-A1-A0SJ-01A-11R-A084-07 LumA 
+## [90m 7[39m  -[31m1[39m[31m.[39m[31m32[39m -[31m31[39m[31m.[39m[31m4[39m  TCGA-A1-A0SK-01A-12R-A084-07 Basal
+## [90m 8[39m  14.8   -[31m6[39m[31m.[39m[31m0[39m[31m5[39m TCGA-A1-A0SM-01A-11R-A084-07 LumA 
+## [90m 9[39m  15.2   -[31m4[39m[31m.[39m[31m74[39m TCGA-A1-A0SN-01A-11R-A144-07 LumB 
+## [90m10[39m -[31m10[39m[31m.[39m[31m3[39m   18.1  TCGA-A1-A0SQ-01A-21R-A144-07 LumA 
 ## [90m# ℹ 241 more rows[39m
 counts_SE.norm.tSNE |>
@@ -788,16 +788,16 @@ 
Test differential cell-type abund
 
## [90m# A tibble: 22 × 6[39m
 ##    .cell_type         cell_type_proportions estimate std.error statistic p.value
 ##    [3m[90m<chr>[39m[23m              [3m[90m<list>[39m[23m                   [3m[90m<dbl>[39m[23m     [3m[90m<dbl>[39m[23m     [3m[90m<dbl>[39m[23m   [3m[90m<dbl>[39m[23m
-## [90m 1[39m cibersort.B.cells… [90m<tibble [48 × 9]>[39m     -[31m2[39m[31m.[39m[31m24[39m        0.791   -[31m2[39m[31m.[39m[31m83[39m   0.004[4m6[24m[4m4[24m
-## [90m 2[39m cibersort.B.cells… [90m<tibble [48 × 9]>[39m     -[31m0[39m[31m.[39m[31m803[39m       0.430   -[31m1[39m[31m.[39m[31m87[39m   0.061[4m9[24m 
-## [90m 3[39m cibersort.Plasma.… [90m<tibble [48 × 9]>[39m     -[31m0[39m[31m.[39m[31m00[39m[31m6[4m4[24m[4m0[24m[39m     0.442   -[31m0[39m[31m.[39m[31m0[39m[31m14[4m5[24m[39m 0.988  
-## [90m 4[39m cibersort.T.cells… [90m<tibble [48 × 9]>[39m      0.049[4m0[24m      0.555    0.088[4m4[24m 0.930  
-## [90m 5[39m cibersort.T.cells… [90m<tibble [48 × 9]>[39m     -[31m1[39m[31m.[39m[31m77[39m        0.553   -[31m3[39m[31m.[39m[31m21[39m   0.001[4m3[24m[4m4[24m
-## [90m 6[39m cibersort.T.cells… [90m<tibble [48 × 9]>[39m      0.236       0.443    0.534  0.593  
-## [90m 7[39m cibersort.T.cells… [90m<tibble [48 × 9]>[39m      2.63        1.38     1.91   0.056[4m1[24m 
-## [90m 8[39m cibersort.T.cells… [90m<tibble [48 × 9]>[39m     -[31m0[39m[31m.[39m[31m841[39m       0.526   -[31m1[39m[31m.[39m[31m60[39m   0.110  
-## [90m 9[39m cibersort.T.cells… [90m<tibble [48 × 9]>[39m      0.959       0.608    1.58   0.114  
-## [90m10[39m cibersort.T.cells… [90m<tibble [48 × 9]>[39m      1.52        0.614    2.47   0.013[4m4[24m 
+## [90m 1[39m cibersort.B.cells… [90m<tibble [48 × 9]>[39m       0.197      0.426     0.464 0.643  
+## [90m 2[39m cibersort.B.cells… [90m<tibble [48 × 9]>[39m      -[31m0[39m[31m.[39m[31m0[39m[31m36[4m2[24m[39m     0.285    -[31m0[39m[31m.[39m[31m127[39m 0.899  
+## [90m 3[39m cibersort.Plasma.… [90m<tibble [48 × 9]>[39m      -[31m0[39m[31m.[39m[31m571[39m      0.350    -[31m1[39m[31m.[39m[31m63[39m  0.103  
+## [90m 4[39m cibersort.T.cells… [90m<tibble [48 × 9]>[39m      -[31m0[39m[31m.[39m[31m569[39m      0.513    -[31m1[39m[31m.[39m[31m11[39m  0.267  
+## [90m 5[39m cibersort.T.cells… [90m<tibble [48 × 9]>[39m      -[31m0[39m[31m.[39m[31m413[39m      0.299    -[31m1[39m[31m.[39m[31m38[39m  0.168  
+## [90m 6[39m cibersort.T.cells… [90m<tibble [48 × 9]>[39m       0.095[4m4[24m     0.265     0.360 0.719  
+## [90m 7[39m cibersort.T.cells… [90m<tibble [48 × 9]>[39m       1.88       0.728     2.59  0.009[4m7[24m[4m2[24m
+## [90m 8[39m cibersort.T.cells… [90m<tibble [48 × 9]>[39m      -[31m0[39m[31m.[39m[31m0[39m[31m42[4m4[24m[39m     0.268    -[31m0[39m[31m.[39m[31m158[39m 0.874  
+## [90m 9[39m cibersort.T.cells… [90m<tibble [48 × 9]>[39m      -[31m0[39m[31m.[39m[31m381[39m      0.378    -[31m1[39m[31m.[39m[31m0[39m[31m1[39m  0.313  
+## [90m10[39m cibersort.T.cells… [90m<tibble [48 × 9]>[39m      -[31m0[39m[31m.[39m[31m230[39m      0.388    -[31m0[39m[31m.[39m[31m591[39m 0.555  
 ## [90m# ℹ 12 more rows[39m

 
We can also perform test of Kaplan-Meier curves.

 
@@ -814,16 +814,16 @@ 
Test differential cell-type abund
 
## [90m# A tibble: 22 × 6[39m
 ##    .cell_type                       cell_type_proportions .low_cellularity_exp…¹
 ##    [3m[90m<chr>[39m[23m                            [3m[90m<list>[39m[23m                                 [3m[90m<dbl>[39m[23m
-## [90m 1[39m cibersort.B.cells.naive          [90m<tibble [48 × 9]>[39m                       11.0
-## [90m 2[39m cibersort.B.cells.memory         [90m<tibble [48 × 9]>[39m                       18.3
-## [90m 3[39m cibersort.Plasma.cells           [90m<tibble [48 × 9]>[39m                       12.3
-## [90m 4[39m cibersort.T.cells.CD8            [90m<tibble [48 × 9]>[39m                       13.4
-## [90m 5[39m cibersort.T.cells.CD4.naive      [90m<tibble [48 × 9]>[39m                       10.4
-## [90m 6[39m cibersort.T.cells.CD4.memory.re… [90m<tibble [48 × 9]>[39m                       12.5
-## [90m 7[39m cibersort.T.cells.CD4.memory.ac… [90m<tibble [48 × 9]>[39m                       14.7
-## [90m 8[39m cibersort.T.cells.follicular.he… [90m<tibble [48 × 9]>[39m                       19.0
-## [90m 9[39m cibersort.T.cells.regulatory..T… [90m<tibble [48 × 9]>[39m                       13.9
-## [90m10[39m cibersort.T.cells.gamma.delta    [90m<tibble [48 × 9]>[39m                       20.1
+## [90m 1[39m cibersort.B.cells.naive          [90m<tibble [48 × 9]>[39m                       9.61
+## [90m 2[39m cibersort.B.cells.memory         [90m<tibble [48 × 9]>[39m                      13.0 
+## [90m 3[39m cibersort.Plasma.cells           [90m<tibble [48 × 9]>[39m                      13.6 
+## [90m 4[39m cibersort.T.cells.CD8            [90m<tibble [48 × 9]>[39m                       9.71
+## [90m 5[39m cibersort.T.cells.CD4.naive      [90m<tibble [48 × 9]>[39m                      11.1 
+## [90m 6[39m cibersort.T.cells.CD4.memory.re… [90m<tibble [48 × 9]>[39m                      11.6 
+## [90m 7[39m cibersort.T.cells.CD4.memory.ac… [90m<tibble [48 × 9]>[39m                      10.4 
+## [90m 8[39m cibersort.T.cells.follicular.he… [90m<tibble [48 × 9]>[39m                      19.5 
+## [90m 9[39m cibersort.T.cells.regulatory..T… [90m<tibble [48 × 9]>[39m                      10.4 
+## [90m10[39m cibersort.T.cells.gamma.delta    [90m<tibble [48 × 9]>[39m                      18.2 
 ## [90m# ℹ 12 more rows[39m
 ## [90m# ℹ abbreviated name: ¹​.low_cellularity_expected[39m
 ## [90m# ℹ 3 more variables: .high_cellularity_expected <dbl>, pvalue <dbl>,[39m
diff --git a/pkgdown.yml b/pkgdown.yml
index 45fda8b1..7611f80d 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -3,5 +3,5 @@ pkgdown: 2.0.9
 pkgdown_sha: ~
 articles:
   introduction: introduction.html
-last_built: 2024-05-16T05:46Z
+last_built: 2024-05-16T05:48Z
 
diff --git a/reference/figures/plot_cluster-1.png b/reference/figures/plot_cluster-1.png
index ea63166b..914031a0 100644
Binary files a/reference/figures/plot_cluster-1.png and b/reference/figures/plot_cluster-1.png differ
diff --git a/reference/figures/unnamed-chunk-14-1.png b/reference/figures/unnamed-chunk-14-1.png
index 0ccf997a..7b71170d 100644
Binary files a/reference/figures/unnamed-chunk-14-1.png and b/reference/figures/unnamed-chunk-14-1.png differ
diff --git a/reference/figures/unnamed-chunk-19-1.png b/reference/figures/unnamed-chunk-19-1.png
index 7ebe3633..2d5100df 100644
Binary files a/reference/figures/unnamed-chunk-19-1.png and b/reference/figures/unnamed-chunk-19-1.png differ
diff --git a/reference/index.html b/reference/index.html
index 04fc2dce..3944ab7f 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -201,6 +201,10 @@ 
All functions rename 

         
         
Rename columns

+      
+          
resolve_complete_confounders_of_non_interest() 

+        
+        
Resolve Complete Confounders of Non-Interest

       
           
rotate_dimensions() 

         
diff --git a/reference/resolve_complete_confounders_of_non_interest-methods.html b/reference/resolve_complete_confounders_of_non_interest-methods.html
new file mode 100644
index 00000000..f0476536
--- /dev/null
+++ b/reference/resolve_complete_confounders_of_non_interest-methods.html
@@ -0,0 +1,132 @@
+
+Resolve Complete Confounders of Non-Interest — resolve_complete_confounders_of_non_interest • tidybulk
+    
+
+    

+      

+
+      
+
+      

+  

+    

+    
Resolve Complete Confounders of Non-Interest

+    Source: R/methods.R, R/methods_SE.R
+    
+    

+
+    

+    
This generic function processes a SummarizedExperiment object to handle confounders
+that are not of interest in the analysis. It dynamically handles combinations
+of provided factors, adjusting the data by nesting and summarizing over these factors.

+    

+
+    

+    
resolve_complete_confounders_of_non_interest(se, ...)
+
+# S4 method for SummarizedExperiment
+resolve_complete_confounders_of_non_interest(se, ...)
+
+# S4 method for RangedSummarizedExperiment
+resolve_complete_confounders_of_non_interest(se, ...)

+    

+
+    

+    
Arguments

+    
se

+
A SummarizedExperiment object that contains the data to be processed.

+
+
+
...

+
Arbitrary number of factor variables represented as symbols or quosures
+to be considered for resolving confounders. These factors are processed
+in combinations of two.

+
+

+    

+    
Value

+    
+
+
A modified SummarizedExperiment object with confounders resolved.

+
+
+
A consistent object (to the input) with additional columns for the statistics from the hypothesis test (e.g.,  log fold change, p-value and false discovery rate).

+
+
+
A consistent object (to the input) with additional columns for the statistics from the hypothesis test (e.g.,  log fold change, p-value and false discovery rate).

+    

+
+    

+    
Examples

+    
# Not run:
+# se is a SummarizedExperiment object
+# resolve_complete_confounders_of_non_interest(se, factor1, factor2, factor3)
+
+

+    

+  

+  
+

+
+
+      

+  
Developed by Stefano Mangiola.

+

+
+

+  
Site built with pkgdown 2.0.9.

+

+
+      

+
+  
+
+
+  
+
+  
+
diff --git a/reference/test_differential_abundance-methods.html b/reference/test_differential_abundance-methods.html
index 57e52eb8..d3a7c607 100644
--- a/reference/test_differential_abundance-methods.html
+++ b/reference/test_differential_abundance-methods.html
@@ -422,7 +422,7 @@ 
Examples

   )
 #> 
 #> n = 5 samples, 2 individuals
-#> Time difference of 31.05561 secs
+#> Time difference of 30.1047 secs
 #> tidybulk says: to access the raw results (fitted GLM) do `attr(..., "internals")$glmmseq_lme4`
 #> class: SummarizedExperiment 
 #> dim: 40 5 
diff --git a/sitemap.xml b/sitemap.xml
index c1192ae1..4eb51aef 100644
--- a/sitemap.xml
+++ b/sitemap.xml
@@ -147,6 +147,9 @@
   
     /reference/rename-methods.html
   
+  
+    /reference/resolve_complete_confounders_of_non_interest-methods.html
+  
   
     /reference/rotate_dimensions-methods.html