formatPHResults: Extract logFC and raw pvalues from multiple post-hoc models...

In DAPAR: Tools for the Differential Analysis of Proteins Abundance with R

Description

Extract logFC and raw pvalues from multiple post-hoc models summaries

Usage

formatPHResults(post_hoc_models_summaries)

Arguments

post_hoc_models_summaries

a list of summaries of post-hoc models.

Value

a list of 2 dataframes containing the logFC values and pvalues for each comparison.

Author(s)

Hélène Borges

Examples

utils::data(Exp1_R25_prot, package='DAPARdata')
obj <- Exp1_R25_prot[1:1000]
keepThat <- mvFilterGetIndices(obj, condition='WholeMatrix', threshold=ncol(obj))
obj <- mvFilterFromIndices(obj, keepThat)
anova_tests <- t(apply(Biobase::exprs(obj),1, classic1wayAnova, conditions=as.factor(Biobase::pData(obj)$Condition)))
names(anova_tests) <- rownames(Biobase::exprs(obj))
tms <- lapply(anova_tests,
             function(x) summary(multcomp::glht(x, linfct = multcomp::mcp(conditions = "Tukey")),
                   test = multcomp::adjusted("none")))
res <- formatPHResults(tms)

DAPAR documentation built on April 11, 2021, 6 p.m.