diff --git a/articles/cTRAP.html b/articles/cTRAP.html index 73c07d8..4093df3 100644 --- a/articles/cTRAP.html +++ b/articles/cTRAP.html @@ -79,7 +79,7 @@

cTRAP: identifying candidate causal

Bernardo P. de Almeida & Nuno Saraiva-Agostinho

-

2024-12-23

+

2024-12-30

Source: vignettes/cTRAP.Rmd @@ -1007,7 +1007,7 @@

Predict targeting drugspredicted <- predictTargetingDrugs(diffExprStat, assoc) 
## Subsetting data based on 11227 intersecting genes (83% of the 13451 input genes)...
## Comparing against 545 CTRP 2.1 compounds (823 cell lines) using 'spearman, pearson, gsea' (gene size of 150)...
-
## Comparison performed in 5.45 secs
+
## Comparison performed in 5.26 secs
 plot(predicted, method="rankProduct")
## Warning: No shared levels found between `names(values)` of the manual scale and the
diff --git a/articles/cTRAP_files/figure-html/unnamed-chunk-4-1.png b/articles/cTRAP_files/figure-html/unnamed-chunk-4-1.png
index f68406b..28d7ab3 100644
Binary files a/articles/cTRAP_files/figure-html/unnamed-chunk-4-1.png and b/articles/cTRAP_files/figure-html/unnamed-chunk-4-1.png differ
diff --git a/pkgdown.yml b/pkgdown.yml
index 107bc05..a12121a 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -3,7 +3,7 @@ pkgdown: 2.1.1
 pkgdown_sha: ~
 articles:
   cTRAP: cTRAP.html
-last_built: 2024-12-23T07:12Z
+last_built: 2024-12-30T07:13Z
 urls:
   reference: https://nuno-agostinho.github.io/cTRAP/reference
   article: https://nuno-agostinho.github.io/cTRAP/articles
diff --git a/reference/ENCODEmetadata.rds b/reference/ENCODEmetadata.rds
index 48a994c..8a9769a 100644
Binary files a/reference/ENCODEmetadata.rds and b/reference/ENCODEmetadata.rds differ
diff --git a/reference/loadExpressionDrugSensitivityAssociation.html b/reference/loadExpressionDrugSensitivityAssociation.html
index bc8380a..6196e92 100644
--- a/reference/loadExpressionDrugSensitivityAssociation.html
+++ b/reference/loadExpressionDrugSensitivityAssociation.html
@@ -25474,7 +25474,7 @@ 
Examples

 #> attr(,"isDrugActivityDirectlyProportionalToSensitivity")
 #> [1] TRUE
 #> attr(,"filename")
-#> [1] "/tmp/RtmpjxkACU/file1d2117a21fc7/reference/expressionDrugSensitivityCorGDSC7.qs"
+#> [1] "/tmp/Rtmpz8y74s/file1d5def92c8d/reference/expressionDrugSensitivityCorGDSC7.qs"
 #> attr(,"class")
 #> [1] "expressionDrugSensitivityAssociation"
 #> [2] "matrix"                              
diff --git a/reference/plot.perturbationChanges.html b/reference/plot.perturbationChanges.html
index 9045b59..85040cb 100644
--- a/reference/plot.perturbationChanges.html
+++ b/reference/plot.perturbationChanges.html
@@ -175,7 +175,7 @@ 
Examples

 compareKD <- rankSimilarPerturbations(diffExprStat, cmapPerturbationsKD)
 #> Subsetting data based on 8790 intersecting genes (65% of the 13451 input genes)...
 #> Comparing against 26 comparisons (1 cell line) using 'spearman, pearson, gsea' (gene size of 150)...
-#> Comparison performed in 0.61 secs
+#> Comparison performed in 0.6 secs
 EIF4G1knockdown <- grep("EIF4G1", compareKD[[1]], value=TRUE)
 plot(cmapPerturbationsKD, EIF4G1knockdown, diffExprStat, method="spearman")
 
diff --git a/reference/plot.referenceComparison.html b/reference/plot.referenceComparison.html
index e9bfa4c..94ced33 100644
--- a/reference/plot.referenceComparison.html
+++ b/reference/plot.referenceComparison.html
@@ -191,7 +191,7 @@ 
Examples

 compareKD <- rankSimilarPerturbations(diffExprStat, cmapPerturbationsKD)
 #> Subsetting data based on 8790 intersecting genes (65% of the 13451 input genes)...
 #> Comparing against 26 comparisons (1 cell line) using 'spearman, pearson, gsea' (gene size of 150)...
-#> Comparison performed in 0.6 secs
+#> Comparison performed in 0.59 secs
 
 # Plot ranked list of CMap perturbations
 plot(compareKD, method="spearman")
@@ -234,7 +234,7 @@ 
Examples

 predicted <- predictTargetingDrugs(diffExprStat, gdsc)
 #> Subsetting data based on 11396 intersecting genes (85% of the 13451 input genes)...
 #> Comparing against 266 GDSC 7 compounds (983 cell lines) using 'spearman, pearson, gsea' (gene size of 150)...
-#> Comparison performed in 2.51 secs
+#> Comparison performed in 2.5 secs
 
 # Plot ranked list of targeting drugs
 plot(predicted, method="spearman")
@@ -269,13 +269,13 @@ 
Examples

 # Plot results for a single targeting drug
 drug <- predicted$compound[[4]]
 plot(predicted, drug, method="spearman")
-#> Loading data from /tmp/RtmpjxkACU/file1d2117a21fc7/reference/expressionDrugSensitivityCorGDSC7.qs...
+#> Loading data from /tmp/Rtmpz8y74s/file1d5def92c8d/reference/expressionDrugSensitivityCorGDSC7.qs...
 
 plot(predicted, drug, method="pearson")
-#> Loading data from /tmp/RtmpjxkACU/file1d2117a21fc7/reference/expressionDrugSensitivityCorGDSC7.qs...
+#> Loading data from /tmp/Rtmpz8y74s/file1d5def92c8d/reference/expressionDrugSensitivityCorGDSC7.qs...
 
 plot(predicted, drug, method="gsea")
-#> Loading data from /tmp/RtmpjxkACU/file1d2117a21fc7/reference/expressionDrugSensitivityCorGDSC7.qs...
+#> Loading data from /tmp/Rtmpz8y74s/file1d5def92c8d/reference/expressionDrugSensitivityCorGDSC7.qs...
diff --git a/reference/plotDrugSetEnrichment.html b/reference/plotDrugSetEnrichment.html index f3e8b32..14df2f0 100644 --- a/reference/plotDrugSetEnrichment.html +++ b/reference/plotDrugSetEnrichment.html @@ -133,7 +133,7 @@

Examples

predicted <- predictTargetingDrugs(diffExprStat, gdsc) #> Subsetting data based on 11396 intersecting genes (85% of the 13451 input genes)... #> Comparing against 266 GDSC 7 compounds (983 cell lines) using 'spearman, pearson, gsea' (gene size of 150)... -#> Comparison performed in 2.51 secs +#> Comparison performed in 2.52 secs plotDrugSetEnrichment(drugSets, predicted) #> Matching compounds with those available in drug sets... diff --git a/reference/plotTargetingDrugsVSsimilarPerturbations.html b/reference/plotTargetingDrugsVSsimilarPerturbations.html index fb8d2b0..82e7347 100644 --- a/reference/plotTargetingDrugsVSsimilarPerturbations.html +++ b/reference/plotTargetingDrugsVSsimilarPerturbations.html @@ -152,7 +152,7 @@

Examples

cmapPerturbationsCompounds) #> Subsetting data based on 8790 intersecting genes (65% of the 13451 input genes)... #> Comparing against 22 CMap perturbations (2 cell lines) using 'spearman, pearson, gsea' (gene size of 150)... -#> Comparison performed in 0.98 secs +#> Comparison performed in 1.19 secs # Predict targeting drugs gdsc <- loadExpressionDrugSensitivityAssociation("GDSC 7") @@ -160,7 +160,7 @@

Examples

predicted <- predictTargetingDrugs(diffExprStat, gdsc) #> Subsetting data based on 11396 intersecting genes (85% of the 13451 input genes)... #> Comparing against 266 GDSC 7 compounds (983 cell lines) using 'spearman, pearson, gsea' (gene size of 150)... -#> Comparison performed in 2.59 secs +#> Comparison performed in 2.64 secs plotTargetingDrugsVSsimilarPerturbations(predicted, similarPerts, "spearman_rank") diff --git a/reference/predictTargetingDrugs.html b/reference/predictTargetingDrugs.html index e53d100..818fb17 100644 --- a/reference/predictTargetingDrugs.html +++ b/reference/predictTargetingDrugs.html @@ -179,7 +179,7 @@

Examples

predictTargetingDrugs(diffExprStat, gdsc) #> Subsetting data based on 11396 intersecting genes (85% of the 13451 input genes)... #> Comparing against 266 GDSC 7 compounds (983 cell lines) using 'spearman, pearson, gsea' (gene size of 150)... -#> Comparison performed in 2.49 secs +#> Comparison performed in 2.51 secs #> compound spearman_coef spearman_pvalue spearman_qvalue pearson_coef #> <char> <num> <num> <num> <num> #> 1: 1047 0.14532331 7.908329e-55 2.103616e-52 0.13098933 diff --git a/reference/rankSimilarPerturbations.html b/reference/rankSimilarPerturbations.html index 1e79371..e370067 100644 --- a/reference/rankSimilarPerturbations.html +++ b/reference/rankSimilarPerturbations.html @@ -197,7 +197,7 @@

Examples

rankSimilarPerturbations(diffExprStat, perturbations) #> Subsetting data based on 8790 intersecting genes (65% of the 13451 input genes)... #> Comparing against 22 CMap perturbations (2 cell lines) using 'spearman, pearson, gsea' (gene size of 150)... -#> Comparison performed in 0.72 secs +#> Comparison performed in 0.69 secs #> compound_perturbation spearman_coef #> <char> <num> #> 1: CVD001_24H:BRD-A14014306-001-01-1:4.1 0.224252829 @@ -311,7 +311,7 @@

Examples

rankSimilarPerturbations(diffExprStat, perturbations, method="spearman") #> Subsetting data based on 8790 intersecting genes (65% of the 13451 input genes)... #> Comparing against 22 CMap perturbations (2 cell lines) using 'spearman'... -#> Comparison performed in 0.5 secs +#> Comparison performed in 0.49 secs #> compound_perturbation spearman_coef #> <char> <num> #> 1: CVD001_24H:BRD-A14014306-001-01-1:4.1 0.224252829