Function reference • YESCDS

All functions
`MA_cancer_rate_table()`	simple tables of confidence intervals for cancer incidence
`SEER_2018`	a data.frame with SEER estimates of cancer incidence for 2018
`brcamutSE`	a SummarizedExperiment collecting BRCA mutations and colData from curatedTCGAData
`build_deck()`	make a deck of cards with 52 elements and unicode symbols for suits
`build_simple_survival_curve()`	utility for survival curve illustration
`build_surv_for_mut()`	use curatedTCGAData to produce survival time structure and mutation matrix for a TCGA tumor type
`canada_crude`	a data.frame with (rounded) crude rates of cancer as presented at https://www.statcan.gc.ca/en/dai/btd/asr
`cancer_map_app()`	use shiny for a simple cancer map, by type, for US
`cancer_map_usa()`	simple function for site-specific map
`cancer_map_world()`	simple map of cancer rates world wide
`compare_tumors()`	compare multiple tumor times with respect to survival
`do_new_surv()`	utility for survival curve, alternate shape
`faces()`	get faces of a collection of cards
`filter_woncan()`	generate site-specific rate table
`full_house()`	test for full house
`has_mut_in()`	check all columns for presence of symbol in a SE with ragged mutation matrix as assay
`is_flush()`	test for flush
`make_comparison()`	make an interactive histogram of rate ratios, or a scatterplot for rate comparisons, between two areas
`make_hist()`	make an interactive histogram for a given cancer site, based on a rate table
`make_pair()`	make interactive beeswarm or box plots for all cancer incidence rates in two areas
`map_app()`	use shiny to explore aspects of geographic mapping
`mass_cancer_map()`	map cancer rates for selected sites to MA counties
`mass_map()`	simple function to display HTML map of MA
`metabric`	a data.frame with clinical features of a breast cancer study (METABRIC) derived from cBioPortal
`one_pair()`	test for one pair
`ordered_seg_cal()`	big display of ordered CIs for California Lung and Bronchus incidence 2014-2018
`plot(<two_sample_mut_surv>)`	plot method
`plot_seer_trend()`	plot the rate statistics over time for selected cancer sites and subgroups
`plotwci()`	simple display of confidence intervals for cancer incidence
`print(<two_sample_mut_surv>)`	print method
`prostate_met_adeno`	a data.frame with clinical features of a metastatic prostate adenocarcinoma study
`show_5y_estimate()`	utility for survival curve illustration: 5y survprob estimate sketch
`show_median_estimate()`	utility for survival curve illustration: median estimate sketch
`statcrunch_msa`	geographic information from statcrunch.com on metropolitan statistical areas
`suits()`	get suits of a collection of cards
`summary(<two_sample_mut_surv>)`	summary method
`table_woncan()`	simplify table view of WONDER CDC statistsics
`two_pairs()`	test for two pairs
`two_sample_surv_setup()`	two-sample survival comparison dependent on mutation present in gene
`us_county_geo`	locations of US counties
`us_map()`	simple function to display HTML map of US
`variation_app()`	simple app to show different ways of examining variation over body sites and MSAs
`vjc_cancer_net`	a table of data of Vince's contacts who developed cancer
`woncan`	cancer rate data by metropolitan statistical area, 1999-2018, from CDC WONDER system
`woncan_meta`	metadata on cancer rate data by metropolitan statistical area, 1999-2018, from CDC WONDER system
`woncan_types()`	generate vector of cancer sites in CDC Wonder table
`world_cancer_2020_all`	a table of cancer rate data by country, retrieved from https://gco.iarc.fr/today/online-analysis-map
`world_geo_sf`	a simple features (sf) instance with boundaries and centroids for 241 countries or other political geographic entities

Reference

All functions