update examples

aertslab · Dec 1, 2022 · 8c0481b · 8c0481b
1 parent f67c7c0
commit 8c0481b
Show file tree

Hide file tree

Showing 6 changed files with 12 additions and 16 deletions.
diff --git a/inst/examples/example_addMotifAnnotation.R b/inst/examples/example_addMotifAnnotation.R
@@ -11,7 +11,8 @@ geneLists <- list(hypoxia=read.table(txtFile, stringsAsFactors=FALSE)[,1])
 #### Databases
 ## Motif rankings: Select according to organism and distance around TSS
 ## (See the vignette for URLs to download)
-# motifRankings <- importRankings("hg19-500bp-upstream-7species.mc9nr.feather")
+# motifRankings <- importRankings("~/databases/hg38_10kbp_up_10kbp_down_full_tx_v10_clust.genes_vs_motifs.rankings.feather")
+# data("motifAnnotations_hgnc") # human TFs (for motif collection 10)
 
 ## For this example we will use a SUBSET of the ranking/motif databases:
 library(RcisTarget.hg19.motifDBs.cisbpOnly.500bp)

diff --git a/inst/examples/example_addSignificantGenes.R b/inst/examples/example_addSignificantGenes.R
@@ -12,6 +12,7 @@ geneLists <- list(hypoxia=read.table(txtFile, stringsAsFactors=FALSE)[,1])
 ## Motif rankings: Select according to organism and distance around TSS
 ## (See the vignette for URLs to download)
 # motifRankings <- importRankings("hg19-500bp-upstream-7species.mc9nr.feather")
+# data("motifAnnotations_hgnc") # human TFs (for motif collection 10)
 
 ## For this example we will use a SUBSET of the ranking/motif databases:
 library(RcisTarget.hg19.motifDBs.cisbpOnly.500bp)

diff --git a/inst/examples/example_aucScores_class.R b/inst/examples/example_aucScores_class.R
@@ -10,17 +10,13 @@ geneLists <- list(hypoxia=read.table(txtFile, stringsAsFactors=FALSE)[,1])
 #### Databases
 ## Motif rankings: Select according to organism and distance around TSS
 ## (See the vignette for URLs to download)
-# motifRankings <- importRankings("hg19-500bp-upstream-7species.mc9nr.feather")
+# motifRankings <- importRankings("~/databases/hg38_10kbp_up_10kbp_down_full_tx_v10_clust.genes_vs_motifs.rankings.feather")
 
 ## For this example we will use a SUBSET of the ranking/motif databases:
 library(RcisTarget.hg19.motifDBs.cisbpOnly.500bp)
 data(hg19_500bpUpstream_motifRanking_cispbOnly)
 motifRankings <- hg19_500bpUpstream_motifRanking_cispbOnly
 
-## Motif - TF annotation:
-data(motifAnnotations_hgnc_v9) # human TFs (for motif collection 9)
-motifAnnotation <- motifAnnotations_hgnc_v9
-
 ### Run RcisTarget
 # Step 1. Calculate AUC
 motifs_AUC <- calcAUC(geneLists, motifRankings)

diff --git a/inst/examples/example_cisTarget.R b/inst/examples/example_cisTarget.R
@@ -11,14 +11,13 @@ txtFile <- paste(file.path(system.file('examples', package='RcisTarget')),
                  "hypoxiaGeneSet.txt", sep="/")
 geneLists <- list(hypoxia=read.table(txtFile, stringsAsFactors=FALSE)[,1])
 
-### Load databases
-# Motif rankings: Select according to organism and distance around TSS
-# (See the vignette for URLs to download)
-motifRankings <- importRankings("hg19-500bp-upstream-7species.mc9nr.feather")
+#### Load databases
+## Motif rankings: Select according to organism and distance around TSS
+## (See the vignette for URLs to download)
+motifRankings <- importRankings("~/databases/hg38_10kbp_up_10kbp_down_full_tx_v10_clust.genes_vs_motifs.rankings.feather")
 
 ## Motif - TF annotation:
-data(motifAnnotations_hgnc_v9) # human TFs (for motif collection 9)
-motifAnnotation <- motifAnnotations_hgnc_v9
+data("motifAnnotations_hgnc") # human TFs (for motif collection 10)
 ##################################################
 
 # Run (R)cisTarget

diff --git a/inst/examples/example_workflow.R b/inst/examples/example_workflow.R
@@ -13,11 +13,10 @@ geneLists <- list(hypoxia=read.table(txtFile, stringsAsFactors=FALSE)[,1])
 #### Load databases
 ## Motif rankings: Select according to organism and distance around TSS
 ## (See the vignette for URLs to download)
-motifRankings <- importRankings("hg19-500bp-upstream-7species.mc9nr.feather")
+motifRankings <- importRankings("~/databases/hg38_10kbp_up_10kbp_down_full_tx_v10_clust.genes_vs_motifs.rankings.feather")
 
 ## Motif - TF annotation:
-data(motifAnnotations_hgnc_v9) # human TFs (for motif collection 9)
-motifAnnotation <- motifAnnotations_hgnc_v9
+data("motifAnnotations_hgnc") # human TFs (for motif collection 10)
 ##################################################
 
 #### Run RcisTarget
@@ -27,7 +26,7 @@ motifs_AUC <- calcAUC(geneLists, motifRankings)
 
 # Step 2. Select significant motifs, add TF annotation & format as table
 motifEnrichmentTable <- addMotifAnnotation(motifs_AUC,
-                         motifAnnot=motifAnnotation)
+                         motifAnnot=motifAnnotations)
 
 # Step 3 (optional). Identify genes that have the motif significantly enriched
 # (i.e. genes from the gene set in the top of the ranking)

diff --git a/inst/examples/motifEnrichmentTable_wGenes.RData b/inst/examples/motifEnrichmentTable_wGenes.RData