create_design: Create design matrix

In bhagwataditya/autonomics: Unified Statistical Modeling of Omics Data

Create design matrix

Description

Create design matrix for statistical analysis

Usage

create_design(object, ...)

## S3 method for class 'SummarizedExperiment'
create_design(
  object,
  formula = default_formula(object),
  drop = varlevels_dont_clash(object, all.vars(formula)),
  codingfun = contr.treatment.explicit,
  verbose = TRUE,
  ...
)

## S3 method for class 'data.table'
create_design(
  object,
  formula = default_formula(object),
  drop = varlevels_dont_clash(object, all.vars(formula)),
  codingfun = contr.treatment.explicit,
  verbose = TRUE,
  ...
)

Arguments

object	SummarizedExperiment or data.frame
...	required to s3ify
formula	formula with svars
drop	whether to drop predictor names
codingfun	factor coding function contr.treatment: intercept = y0, coefi = yi - y0 contr.treatment.explicit: intercept = y0, coefi = yi - y0 code_control: intercept = ymean, coefi = yi - y0 contr.diff: intercept = y0, coefi = yi - y(i-1) code_diff: intercept = ymean, coefi = yi - y(i-1) code_diff_forward: intercept = ymean, coefi = yi - y(i+) code_deviation: intercept = ymean, coefi = yi - ymean (drop last) code_deviation_first: intercept = ymean, coefi = yi - ymean (drop first) code_helmert: intercept = ymean, coefi = yi - mean(y0:(yi-1)) code_helmert_forward: intercept = ymean, coefi = yi - mean(y(i+1):yp)
verbose	whether to message

Value

design matrix

Examples

file <- system.file('extdata/atkin.metabolon.xlsx', package = 'autonomics')
object <- read_metabolon(file)
unique(create_design(object))
unique(create_design(object, ~ Time))
unique(create_design(object, ~ Time, codingfun = contr.treatment.explicit))
unique(create_design(object, ~ Time, codingfun = contr.diff))
unique(create_design(object, ~ Time + Diabetes))
unique(create_design(object, ~ Time / Diabetes))
unique(create_design(object, ~ Time * Diabetes))

bhagwataditya/autonomics documentation built on Dec. 1, 2024, 12:27 a.m.