topFeatures {msqrob2} | R Documentation

## Toplist of DE proteins, peptides or features

### Description

Summary table of the differentially expressed Features

### Usage

    topFeatures(models, contrast, adjust.method = "BH", sort = TRUE, alpha = 1)

### Arguments

`models` | A list with elements of the class `StatModel` that are estimated using the `msqrob` function
`contrast` | `numeric` (matrix)vector specifying one contrast of the linear model coefficients to be tested equal to zero. The (row)names of the vector should be equal to the names of parameters of the model.
`adjust.method` | `character` specifying the method to adjust the p-values for multiple testing. Options, in increasing conservatism, include ‘"none"’, ‘"BH"’, ‘"BY"’ and ‘"holm"’. See ‘p.adjust’ for the complete list of options. Default is "BH" the Benjamini-Hochberg method to controle the False Discovery Rate (FDR).
`sort` | `boolean(1)` to indicate if the features have to be sorted according to statistical significance.
`alpha` | `numeric` specifying the cutoff value for adjusted p-values. Only features with lower p-values are listed.

### Value

A dataframe with log2 fold changes (logFC), standard errors (se), degrees of freedom of the test (df), t-test statistic (t), p-values (pval) and adjusted pvalues (adjPval) using the specified adjust.method in the p.adjust function of the stats package.

### Author(s)

Lieven Clement

### Examples

    data(pe)

    # Aggregate peptide intensities in protein expression values
    pe <- aggregateFeatures(pe, i = "peptide", fcol = "Proteins", name = "protein")

    # Fit msqrob model
    pe <- msqrob(pe, i = "protein", formula = ~condition)

    # Define contrast
    getCoef(rowData(pe[["protein"]])$msqrobModels[[1]])

    # Assess log2 fold change between condition c and condition b:
    L <- makeContrast("conditionc - conditionb=0", c("conditionb", "conditionc"))
    topDeProteins <- topFeatures(rowData(pe[["protein"]])$msqrobModels, L)

[Package msqrob2 version 1.2.0 Index]