add_adjusted_pvalues: Add adjusted pvalues

In bhagwataditya/importomics: Unified statistal Modeling of Omics Data

Add adjusted pvalues

Description

Add adjusted pvalues

Usage

add_adjusted_pvalues(
  featuredt,
  method,
  fit = fits(featuredt),
  coefs = default_coefs(featuredt, fit = fit),
  verbose = TRUE
)

Arguments

featuredt	fdt(object)
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/importomics documentation built on Oct. 29, 2024, 3:19 p.m.