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t-test

Source: R/ttest_class.R
ttest.Rd

A t-test compares the means of two factor levels. Multiple-test corrected p-values are used to indicate the significance of the computed difference for all features.

Usage

ttest(
  alpha = 0.05,
  mtc = "fdr",
  factor_names,
  paired = FALSE,
  paired_factor = character(0),
  equal_variance = FALSE,
  conf_level = 0.95,
  control_group = NULL,
  ...
)

Arguments

alpha

(numeric) The p-value cutoff for determining significance. The default is 0.05.

mtc

(character) Multiple test correction method. Allowed values are limited to the following:

  • "bonferroni": Bonferroni correction in which the p-values are multiplied by the number of comparisons.

  • "fdr": Benjamini and Hochberg False Discovery Rate correction.

  • "none": No correction.

The default is "fdr".

factor_names

(character) The name of sample meta column(s) to use.

paired

(logical) Apply a paired t-test. The default is FALSE.

paired_factor

(character) The factor name that encodes the sample id for pairing. The default is character(0).

equal_variance

(logical) Equal variance. Allowed values are limited to the following:

  • "TRUE": The variance of each group is treated as being equal using the pooled variance to estimate the variance.

  • "FALSE": The variance of each group is not assumed to be equal and the Welch (or Satterthwaite) approximation is used.

The default is FALSE.

conf_level

(numeric) The confidence level of the interval. The default is 0.95.

control_group

(character, NULL) The level name of the group used as the second group (where possible) when computing t-statistics. This ensures a positive t-statistic corresponds to an increase when compared to the control group. The default is NULL.

...

Additional slots and values passed to struct_class.

Value

A ttest object with the following output slots:

t_statistic(data.frame) The value of the calculate statistics which is converted to a p-value when compared to a t-distribution.
p_value(data.frame) The probability of observing the calculated t-statistic.
dof(numeric) The number of degrees of freedom used to calculate the test statistic.
significant(data.frame) TRUE if the calculated p-value is less than the supplied threhold (alpha).
conf_int(data.frame) Confidence interval for t statistic.
estimates(data.frame) The group means estimated when computing the t-statistic.

Inheritance

A ttest object inherits the following struct classes:

[ttest] >> [model] >> [struct_class]

Examples

M = ttest(
      alpha = 0.05,
      mtc = "fdr",
      factor_names = "V1",
      paired = FALSE,
      paired_factor = "NA",
      equal_variance = FALSE,
      conf_level = 0.95,
      control_group = NULL)

M = ttest(factor_name='Class')