subset_by_frequency: Subset a Binary Matrix By Alteration Frequency Threshold

In AxelitoMartin/gnomeR: Wrangle and analyze IMPACT and TCGA mutation data

Subset a Binary Matrix By Alteration Frequency Threshold

Description

Subset a Binary Matrix By Alteration Frequency Threshold

Usage

subset_by_frequency(gene_binary, t = 0.1, other_vars = NULL)

Arguments

gene_binary	A data frame with a row for each sample and column for each alteration. Data frame must have a sample_id column and columns for each alteration with values of 0, 1 or NA.
t	Threshold value between 0 and 1 to subset by. Default is 10% (.1).
other_vars	One or more column names (quoted or unquoted) in data to be retained in resulting data frame. Default is NULL.

Value

a data frame with a sample_id column and columns for alterations over the given prevalence threshold of t.

Examples

samples <- unique(gnomeR::mutations$sampleId)
 gene_binary <- create_gene_binary(
   samples = samples, mutation = mutations, cna = cna,
   mut_type = "somatic_only",
   include_silent = FALSE,
   specify_panel = "impact"
 )
gene_binary %>%
 subset_by_frequency()

AxelitoMartin/gnomeR documentation built on March 23, 2024, 3:07 a.m.