# #——安装、eval = FALSE - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # install.packages (BiocManager) # BiocManager::安装(“psichomics”) # # - - - - - eval = FALSE - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - #库(psichomics) # psichomics() # #——回声= FALSE, fig.retina =零。宽度= 400 pt, fig.cap = "选项TCGA加载数据。”- - - - - knitr:: include_graphics (img / 1 _load_data.png) # #——回声= FALSE, fig.retina =零。宽度= 400 pt, fig.cap = "选项过滤和正常化基因表达。”- - - - - knitr:: include_graphics (img / 2 _normalise_gene_expression.png) # #——回声= FALSE, fig.retina =零。宽度= 400 pt, fig.cap = "选项来量化可变剪接。”- - - - - knitr:: include_graphics (img / 3 _quantify_splicing.png) # #——回声= FALSE, fig.retina =零。宽度= 400 pt, fig.cap =“创建组肿瘤的阶段。”- - - - - knitr:: include_graphics (img / 4 _data_grouping.png) # #——回声= FALSE, fig.retina =零。宽度= 600 pt, fig.cap = "表显示数据组为下游创建分析。”- - - - - knitr:: include_graphics (img / 4 _group_tables.png) # #——回声= FALSE, fig.retina =零。宽度= 400 pt, fig.cap = "选项保存和加载组。”- - - - - knitr:: include_graphics (img / 4 _save_groups.png) # #——回声= FALSE, fig.retina =零。宽度= 800 pt, fig.cap = "选项来执行和想象PCA。”- - - - - knitr:: include_graphics (img / 5 _pca.png) # #——回声= FALSE, fig.retina =零。宽度= 400 pt, fig.cap =“PCA分数和加载块”——knitr:: include_graphics (“img / pca_results.png”) # #——回声= FALSE, fig.retina =零。宽度= 400 pt, fig.cap = " *麻木*外显子剪接差12肿瘤与正常样本。”——knitr:: include_graphics (img / NUMB_exon_12_inclusion.png) # #——回声= FALSE, fig.retina =零。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")