diff --git a/vignettes/MotifPeeker.Rmd b/vignettes/MotifPeeker.Rmd index 00165b3..710c2af 100644 --- a/vignettes/MotifPeeker.Rmd +++ b/vignettes/MotifPeeker.Rmd @@ -186,25 +186,27 @@ The report can be generated by using the main function `MotifPeeker()`. For more run customisations, refer to the next sections. ```{r run-motifpeeker} -MotifPeeker( - peak_files = peak_files, - reference_index = 2, # Set TIP-seq experiment as reference - alignment_files = alignment_files, - exp_labels = c("ChIP", "TIP"), - exp_type = c("chipseq", "tipseq"), - genome_build = "hg38", # Use hg38 genome build - motif_files = motif_files, - cell_counts = NULL, # No cell-count information - denovo_motif_discovery = TRUE, - denovo_motifs = 3, # Discover top 3 motifs - motif_db = NULL, # Use default motif database (JASPAR) - download_buttons = TRUE, - out_dir = tempdir(), # Save output in a temporary directory - workers = 2, # Use two CPU cores on a 16GB RAM machine - debug = FALSE, - quiet = TRUE, - verbose = TRUE -) +if (MotifPeeker:::confirm_meme_install(continue = TRUE)) { + MotifPeeker( + peak_files = peak_files, + reference_index = 2, # Set TIP-seq experiment as reference + alignment_files = alignment_files, + exp_labels = c("ChIP", "TIP"), + exp_type = c("chipseq", "tipseq"), + genome_build = "hg38", # Use hg38 genome build + motif_files = motif_files, + cell_counts = NULL, # No cell-count information + denovo_motif_discovery = TRUE, + denovo_motifs = 3, # Discover top 3 motifs + motif_db = NULL, # Use default motif database (JASPAR) + download_buttons = TRUE, + out_dir = tempdir(), # Save output in a temporary directory + workers = 2, # Use two CPU cores on a 16GB RAM machine + debug = FALSE, + quiet = TRUE, + verbose = TRUE + ) +} ``` ### Required Inputs