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create.stats - perform statistical analysis and generate an output data.table

Source: R/create.stats.R
create.stats.Rd

This function performs statistical analysis and generates an output data.table

Usage

create.stats(
  dat,
  use.cols,
  sample.col,
  group.col,
  comparisons,
  variance.test = "kruskal.test",
  pairwise.test = "wilcox.test",
  corrections = "fdr"
)

Arguments

dat

NO DEFAULT. A data.table containing summary data (samples vs features)

use.cols

NO DEFAULT. Columns (i.e. features) to use for statistical analysis.

sample.col

NO DEFAULT. The column denoting sample names.

group.col

NO DEFAULT. The column denoting experimental group names.

comparisons

NO DEFAULT. A list of pairwise comparisons between samples. E.g. list(c('Group A', 'Group B'), c('Group B', 'Group C')).

variance.test

DEFAULT = 'kruskal.test'. Currently the only option

pairwise.test

DEFAULT = 'wilcox.test'. Currently the only option

corrections

DEFAULT = 'fdr' (false discovery rate). Currently the only option

References

https://github.com/ImmuneDynamics/Spectre.

Author

Thomas M Ashhurst, thomas.ashhurst@sydney.edu.au