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tbl_genomic

Source: R/tbl_genomic.R
tbl_genomic.Rd

This function will select genes based on user inputs or on frequency counts and then will pass the data.frame to gtsummary::tbl_summary(). You can specify a by variable and other parameters that are accepted by gtsummary::tbl_summary(). Note the by variable must be merged on to onto the data before using the by parameter in the function.

Usage

tbl_genomic(
  gene_binary,
  by = NULL,
  freq_cutoff = deprecated(),
  freq_cutoff_by_gene = deprecated(),
  gene_subset = deprecated(),
  ...
)

Arguments

gene_binary

data.frame of genetic samples

by

A variable to be passed to gtsummary::tbl_summary()'s by parameter

freq_cutoff

deprecated

freq_cutoff_by_gene

deprecated

gene_subset

deprecated

...

Additional parameters that can be passed to gtsummary::tbl_summary(). To access the additional parameters you need to load gtsummary.

Value

A tbl_summary() object

Examples


samples <- unique(mutations$sampleId)[1:10]

gene_binary <- create_gene_binary(
  samples = samples,
  mutation = gnomeR::mutations,
  cna = gnomeR::cna,
  mut_type = "somatic_only", snp_only = FALSE,
  specify_panel = "no"
)

tbl1 <- tbl_genomic(gene_binary)

# Example wth `by` variable

gene_binary$sex <- sample( c("M", "F"), size = nrow(gene_binary), replace = TRUE)

tbl2 <- tbl_genomic(
  gene_binary = gene_binary,
  by = sex
) %>%
gtsummary::add_p() %>%
gtsummary::add_q()
#> The following errors were returned during `::()`, `gtsummary()`, and `add_q()`:
#> ✖ For variable `AKT1` (`sex`) and "p.value" statistic: The package "cardx" (>=
#>   0.2.1) is required.
#> ✖ For variable `ALK` (`sex`) and "p.value" statistic: The package "cardx" (>=
#>   0.2.1) is required.
#> ✖ For variable `APC` (`sex`) and "p.value" statistic: The package "cardx" (>=
#>   0.2.1) is required.
#> ✖ For variable `AR.Amp` (`sex`) and "p.value" statistic: The package "cardx"
#>   (>= 0.2.1) is required.
#> ✖ For variable `ASXL2` (`sex`) and "p.value" statistic: The package "cardx" (>=
#>   0.2.1) is required.
#> ✖ For variable `BRCA2` (`sex`) and "p.value" statistic: The package "cardx" (>=
#>   0.2.1) is required.
#> ✖ For variable `CARD11` (`sex`) and "p.value" statistic: The package "cardx"
#>   (>= 0.2.1) is required.
#> ✖ For variable `CTNNB1` (`sex`) and "p.value" statistic: The package "cardx"
#>   (>= 0.2.1) is required.
#> ✖ For variable `EPHB1` (`sex`) and "p.value" statistic: The package "cardx" (>=
#>   0.2.1) is required.
#> ✖ For variable `FAT1` (`sex`) and "p.value" statistic: The package "cardx" (>=
#>   0.2.1) is required.
#> ✖ For variable `FGFR1.Amp` (`sex`) and "p.value" statistic: The package "cardx"
#>   (>= 0.2.1) is required.
#> ✖ For variable `IRS2` (`sex`) and "p.value" statistic: The package "cardx" (>=
#>   0.2.1) is required.
#> ✖ For variable `JAK1` (`sex`) and "p.value" statistic: The package "cardx" (>=
#>   0.2.1) is required.
#> ✖ For variable `KDM6A.Del` (`sex`) and "p.value" statistic: The package "cardx"
#>   (>= 0.2.1) is required.
#> ✖ For variable `KMT2C` (`sex`) and "p.value" statistic: The package "cardx" (>=
#>   0.2.1) is required.
#> ✖ For variable `KMT2D` (`sex`) and "p.value" statistic: The package "cardx" (>=
#>   0.2.1) is required.
#> ✖ For variable `MYC` (`sex`) and "p.value" statistic: The package "cardx" (>=
#>   0.2.1) is required.
#> ✖ For variable `MYC.Amp` (`sex`) and "p.value" statistic: The package "cardx"
#>   (>= 0.2.1) is required.
#> ✖ For variable `NBN.Amp` (`sex`) and "p.value" statistic: The package "cardx"
#>   (>= 0.2.1) is required.
#> ✖ For variable `NF1` (`sex`) and "p.value" statistic: The package "cardx" (>=
#>   0.2.1) is required.
#> ✖ For variable `NKX3-1.Del` (`sex`) and "p.value" statistic: The package
#>   "cardx" (>= 0.2.1) is required.
#> ✖ For variable `PARP1` (`sex`) and "p.value" statistic: The package "cardx" (>=
#>   0.2.1) is required.
#> ✖ For variable `PDGFRA` (`sex`) and "p.value" statistic: The package "cardx"
#>   (>= 0.2.1) is required.
#> ✖ For variable `PIK3R2` (`sex`) and "p.value" statistic: The package "cardx"
#>   (>= 0.2.1) is required.
#> ✖ For variable `PIK3R3` (`sex`) and "p.value" statistic: The package "cardx"
#>   (>= 0.2.1) is required.
#> ✖ For variable `PPP2R1A` (`sex`) and "p.value" statistic: The package "cardx"
#>   (>= 0.2.1) is required.
#> ✖ For variable `PTPRS.Del` (`sex`) and "p.value" statistic: The package "cardx"
#>   (>= 0.2.1) is required.
#> ✖ For variable `RECQL4.Amp` (`sex`) and "p.value" statistic: The package
#>   "cardx" (>= 0.2.1) is required.
#> ✖ For variable `ROS1` (`sex`) and "p.value" statistic: The package "cardx" (>=
#>   0.2.1) is required.
#> ✖ For variable `SMAD2` (`sex`) and "p.value" statistic: The package "cardx" (>=
#>   0.2.1) is required.
#> ✖ For variable `SOX17.Amp` (`sex`) and "p.value" statistic: The package "cardx"
#>   (>= 0.2.1) is required.
#> ✖ For variable `SPEN` (`sex`) and "p.value" statistic: The package "cardx" (>=
#>   0.2.1) is required.
#> ✖ For variable `SPOP` (`sex`) and "p.value" statistic: The package "cardx" (>=
#>   0.2.1) is required.
#> ✖ For variable `TP53` (`sex`) and "p.value" statistic: The package "cardx" (>=
#>   0.2.1) is required.
#> ✖ For variable `TRAF7.Amp` (`sex`) and "p.value" statistic: The package "cardx"
#>   (>= 0.2.1) is required.
#> ✖ For variable `TSC2.Amp` (`sex`) and "p.value" statistic: The package "cardx"
#>   (>= 0.2.1) is required.