## ----------------------------------------------------------------------------- library("OncoScore") ## ----------------------------------------------------------------------------- query = perform.query(c("ASXL1","IDH1","IDH2","SETBP1","TET2")) ## ----------------------------------------------------------------------------- combine.query.results(query, c('IDH1', 'IDH2'), 'new_gene') ## ----eval=FALSE--------------------------------------------------------------- # chr13 = get.genes.from.biomart(chromosome=13,start=54700000,end=72800000) ## ----eval=FALSE--------------------------------------------------------------- # result = compute.oncoscore.from.region(10, 100000, 500000) ## ----------------------------------------------------------------------------- result = compute.oncoscore(query) ## ----------------------------------------------------------------------------- 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")) ## ----------------------------------------------------------------------------- result.timeseries = compute.oncoscore.timeseries(query.timepoints) ## ----fig.width=12, fig.height=8, warning=FALSE, fig.cap="Oncogenetic potential of the considered genes."---- plot.oncoscore(result, col = 'darkblue') ## ----fig.width=12, fig.height=8, warning=FALSE, fig.cap="Absolute values of the oncogenetic potential of the considered genes over times."---- plot.oncoscore.timeseries(result.timeseries) ## ----fig.width=12, fig.height=8, warning=FALSE, fig.cap="Variations of the oncogenetic potential of the considered genes over times."---- plot.oncoscore.timeseries(result.timeseries, incremental = TRUE, ylab='absolute variation') ## ----fig.width=12, fig.height=8, warning=FALSE, fig.cap="Variations as relative values of the oncogenetic potential of the considered genes over times."---- plot.oncoscore.timeseries(result.timeseries, incremental = TRUE, relative = TRUE, ylab='relative variation')