drop_low_columns: Drop my_dt columns are below a certain percentile in value.

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

Drop my_dt columns are below a certain percentile in value.

Description

Specifies a function to calculate the value of the column and a percentile, below which samples will be dropped.

Usage

drop_low_columns(
  my_dt = NULL,
  col_names = NULL,
  col_value = median,
  my_summary = "Drop low expressing columns.",
  sample_key = get_default_sample_key(),
  percentile_cutoff = 10,
  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
col_value	Function that describes how column values are computed
my_summary	Character string to change the default comment that will be appended to my_dt.
sample_key	Character string to specify the column that is the sample key. This column will not be operated upon.
percentile_cutoff	Numeric percentile. Columns below this percentile will be dropped
readme_path	Optional path to which the comments will be appended.

Details

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ drop_low_columns ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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