add_adjusted_pvalues: Add adjusted pvalues

In bhagwataditya/autonomics: Unified Statistical Modeling of Omics Data

Add adjusted pvalues

Description

Add adjusted pvalues

Usage

add_adjusted_pvalues(object, ...)

## S3 method for class 'data.table'
add_adjusted_pvalues(
  object,
  method = "fdr",
  fit = fits(object),
  coefs = default_coefs(object, fit = fit),
  verbose = TRUE,
  ...
)

## S3 method for class 'SummarizedExperiment'
add_adjusted_pvalues(
  object,
  method = "fdr",
  fit = fits(object),
  coefs = default_coefs(object, fit = fit),
  verbose = TRUE,
  ...
)

Arguments

object	SummarizedExperiment or (feature) data.table
...	for s3 dispatch
method	'fdr', 'bonferroni', ... (see 'p.adjust.methods')
fit	'limma', 'lm', 'lme', 'lmer'
coefs	coefficient (string)
verbose	TRUE or FALSE

Value

SummarizedExperiment

Examples

file <- system.file('extdata/fukuda20.proteingroups.txt', package = 'autonomics')
object <- read_maxquant_proteingroups(file)
fdt(object) %<>% extract(, 1:2)
object %<>% fit_limma(coef = 'Adult-X30dpt')
object %<>% extract(order(fdt(.)$`p~Adult-X30dpt~limma`), )
 fdt(object)
(fdt(object) %<>% add_adjusted_pvalues('fdr'))
(fdt(object) %<>% add_adjusted_pvalues('fdr'))      # smart enough not to add second column
(fdt(object)  %>% add_adjusted_pvalues('bonferroni'))

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