formatPHResults {DAPAR} | R Documentation

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

### 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]
    level <- obj@experimentData@other$typeOfData
    metacell.mask <- match.metacell(GetMetacell(obj), 'missing', level)
    indices <- GetIndices_WholeMatrix(metacell.mask, op='>=', th=1)
    obj <- MetaCellFiltering(obj, indices, cmd='delete')
    anova_tests <- t(apply(Biobase::exprs(obj$new),1, classic1wayAnova,
    conditions=as.factor(Biobase::pData(obj$new)$Condition)))
    names(anova_tests) <- rownames(Biobase::exprs(obj$new))
    tms <- lapply(anova_tests,
                 function(x) summary(multcomp::glht(x,
                 linfct = multcomp::mcp(conditions = "Tukey")),
                       test = multcomp::adjusted("none")))
    res <- formatPHResults(tms)

[Package DAPAR version 1.24.8 Index]