require_data_in_samples: Drop my_dt columns that aren't present in certain...

In Benjamin-Vincent-Lab/binfotron: Binfotron Bioinformatics Analysis Tools Suite

Drop my_dt columns that aren't present in certain percentage_of_samples according to requirement function

Description

Allows you drop columns that don't meet criteria for X

Usage

require_data_in_samples(
  my_dt = NULL,
  col_names = NULL,
  my_summary = "Require data in smaples",
  percentage_of_samples = 75,
  requirement = function(x) {
     sum(x > 0)
 },
  sample_key = get_default_sample_key(),
  readme_path = NULL
)

Arguments

my_dt	data.table input
col_names	Vector of character strings to name the columns that will have this operation performed on them. Uses operatable_columns
my_summary	Character string to change the default comment that will be appended to my_dt.
percentage_of_samples	Percentage of samples that will need to meet the requirement to keep the column
requirement	Function by which to judge the column. For example the default (function(x){sum(x>0)}) requires that the value be greater than zero in 75 percent of the samples.
sample_key	Character string to specify the column that is the sample key. This column will not be operated upon.
readme_path	Optional path to which the comments will be appended.

Details

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ require_data_in_samples ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Benjamin-Vincent-Lab/binfotron documentation built on Oct. 1, 2024, 8:33 p.m.