tbl_genomic | R Documentation |
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.
tbl_genomic(
gene_binary,
by = NULL,
freq_cutoff = deprecated(),
freq_cutoff_by_gene = deprecated(),
gene_subset = deprecated(),
...
)
gene_binary |
data.frame of genetic samples |
by |
A variable to be passed to |
freq_cutoff |
deprecated |
freq_cutoff_by_gene |
deprecated |
gene_subset |
deprecated |
... |
Additional parameters that can be passed to |
A tbl_summary()
object
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()
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