## ----样式-Knitr，eval = true，echo = false，结果=“ asis” -------------------------------------------------------------------------------------------------------- BiocStyle :: lastx（）## --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- library(OncoScore) ## ----评估= false -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------“ tet2”）## ---- include = false，echo = false -------------------------------------------------------------------------------------------------------------------------------------------------数据（查询）## ------------------------------------------------------------------------------------------------------------------------------------------------------------- combine.query.results(query, c('IDH1', 'IDH2'), 'new_gene') ## ----eval=FALSE------------------------------------------------------------------------------------------------------- # chr13 = get.genes.from.biomart(chromosome=13,start=54700000,end=72800000) # head(chr13) ## ----eval=FALSE--------------------------------------------------------------------------------------------------------------＃结果= Compute.Oncoscore.From.Region（10，100000，500000）## -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- result = compute.oncoscore(query) ## ----eval=FALSE--------------------------------------------------------------------- # query.timepoints = perform.query.timeseries(c("ASXL1","IDH1","IDH2","SETBP1","TET2"), # c("2012/03/01", "2013/03/01", "2014/03/01", "2015/03/01", "2016/03/01")) ## ----include=FALSE,echo=FALSE------------------------------------------------------- data(query.timepoints) ## ----------------------------------------------------------------------------------- result.timeseries = compute.oncoscore.timeseries(query.timepoints) ## ----image-oncoscore, fig.show='hide', fig.width=5, fig.height=5, results='hide'---- plot.oncoscore(result, col = 'darkblue') ## ----image-timeseries, fig.show='hide', fig.width=5, fig.height=5, results='hide'---- plot.oncoscore.timeseries(result.timeseries) ## ----image-oncoscore-timeseries, fig.show='hide', fig.width=7, fig.height=5.5, results='hide'---- plot.oncoscore.timeseries(result.timeseries, incremental = TRUE, ylab='absolute variation') ## ----image-oncoscore-timeseries-incremental, fig.show='hide', fig.width=7, fig.height=6.5, results='hide'---- plot.oncoscore.timeseries(result.timeseries, incremental = TRUE, relative = TRUE, ylab='relative variation') ## ----sessioninfo, results='asis', echo=FALSE---------------------------------------- toLatex(sessionInfo())