## ----install, eval=FALSE------------------------------------------------------ # install.packages("BiocManager") # BiocManager::install("psichomics") ## ----eval=FALSE--------------------------------------------------------------- # library(psichomics) # psichomics() ## ----echo=FALSE, fig.retina=NULL, out.width='400pt', fig.cap="Options to load TCGA data."---- knitr::include_graphics("img/1_load_data.png") ## ----echo=FALSE, fig.retina=NULL, out.width='400pt', fig.cap="Options to filter and normalise gene expression."---- knitr::include_graphics("img/2_normalise_gene_expression.png") ## ----echo=FALSE, fig.retina=NULL, out.width='400pt', fig.cap="Options to quantify alternative splicing."---- knitr::include_graphics("img/3_quantify_splicing.png") ## ----echo=FALSE, fig.retina=NULL, out.width='400pt', fig.cap="Creating groups by tumour stage."---- knitr::include_graphics("img/4_data_grouping.png") ## ----echo=FALSE, fig.retina=NULL, out.width='600pt', fig.cap="Table showing data groups as created for downstream analyses."---- knitr::include_graphics("img/4_group_tables.png") ## ----echo=FALSE, fig.retina=NULL, out.width='400pt', fig.cap="Options to save and load groups."---- knitr::include_graphics("img/4_save_groups.png") ## ----echo=FALSE, fig.retina=NULL, out.width='800pt', fig.cap="Options to perform and visualise PCA."---- knitr::include_graphics("img/5_pca.png") ## ----echo=FALSE, fig.retina=NULL, out.width='400pt', fig.cap="PCA score and loading plots"---- knitr::include_graphics("img/pca_results.png") ## ----echo=FALSE, fig.retina=NULL, out.width='400pt', fig.cap="Differential splicing of *NUMB* exon 12 between tumour and normal samples."---- knitr::include_graphics("img/NUMB_exon_12_inclusion.png") ## ----echo=FALSE, fig.retina=NULL, out.width='400pt', fig.cap="Correlation between *NUMB* exon 12 inclusion and QKI expression in all TCGA breast samples."---- knitr::include_graphics("img/Correlation_NUMB_exon_12_and_QKI_GE.png") ## ----echo=FALSE, fig.retina=NULL, out.width='800pt', fig.cap="Differentially spliced events (|Δ Median PSI| > 0.1 and Wilcoxon q-value ≤ 0.01). Labelled splicing events have putative prognostic value (more on that in the following section)."---- knitr::include_graphics("img/diff_analyses.png") ## ----echo=FALSE, fig.retina=NULL, out.width='800pt', fig.cap="Differentially expressed genes (|log2(Fold-change)| > 1 and FDR ≤ 0.01). Labelled genes are those with alternative splicing events with putative prognostic value."---- knitr::include_graphics("img/diff_expression.png") ## ----echo=FALSE, fig.retina=NULL, out.width='400pt', fig.cap="Differential splicing of *UHRF2* exon 10 between tumour stage I and normal samples."---- knitr::include_graphics("img/UHRF2_exon_10_inclusion_differential_splicing.png") ## ----echo=FALSE, fig.retina=NULL, out.width='400pt', fig.cap="Prognostic value of *UHRF2* exon 10 inclusion (patients separated by the optimal PSI cutoff of 0.09)."---- knitr::include_graphics("img/UHRF2_exon_10_inclusion_prognosis.png") ## ----echo=FALSE, fig.retina=NULL, out.width='400pt', fig.cap="Differential expression of *UHRF2* between tumour stage I and normal samples."---- knitr::include_graphics("img/UHRF2_differential_expression.png") ## ----echo=FALSE, fig.retina=NULL, out.width='400pt', fig.cap="Prognostic value of *UHRF2* expression (patients separated by the optimal gene expression cutoff of 5.43)."---- knitr::include_graphics("img/UHRF2_expression_prognosis.png")