tbl_genomic: tbl_genomic

In MSKCC-Epi-Bio/gnomeR: Wrangle and analyze IMPACT and TCGA mutation data

tbl_genomic

Description

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()

MSKCC-Epi-Bio/gnomeR documentation built on Oct. 17, 2024, 3:39 p.m.