below_max_cutoff: Detect samples below a specified cutoff value
In bryancquach/omixjutsu: Utilities for omics analysis tasks

below_max_cutoff

R Documentation

Detect samples below a specified cutoff value

Description

Identify samples with values below a maximum cutoff value.

Usage

below_max_cutoff(
  metrics_table,
  metric,
  cutoff = NULL,
  include_equals = F,
  na_as_false = F,
  coef = 1.7,
  use_unskewed_iqr = F,
  use_skewed_iqr = F
)

Arguments

`metrics_table`	Data frame or matrix with metrics as columns and samples as rows.
`metric`	Name of column with metric to use.
`cutoff`	Cutoff value.
`include_equals`	If `TRUE`, designate metric values equal to cutoff value as TRUE.
`na_as_false`	If `TRUE`, designate comparisons to 'NA' values as FALSE.
`coef`	Constant to multiply the interquartile range by in calculating a relative cutoff. The default value of 1.7 approximately equates to values at least 3 standard deviations from the mean for a gaussian distribution.
`use_unskewed_iqr`	If `TRUE`, set a relative cutoff value using the interquartile range of the metric distribution multiplied by `coef`. More suitable for non-skewed distributions.
`use_skewed_iqr`	If `TRUE`, set relative cutoff value using a medcouple-based adjustment of the interquartile range of the metric distribution multipled by `coef`. More suitable for skewed distributions.

Details

Indicates whether a sample is below a maximum cutoff value for a user-specified metric. Includes options to set the cutoff using values derived from interquartile range for both skewed and unskewed distributions.

Value

A list containing the following elements:

keep a logical vector indicating whether a given value for a metric meets the designated cutoff criteria. The vector order matches the input row order of metrics_table.
cutoff The cutoff value used.