topTable: Toplist of DE proteins, peptides or features

In statOmics/msqrob2: Robust statistical inference for quantitative LC-MS proteomics

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)

statOmics/msqrob2 documentation built on Dec. 21, 2024, 8:26 a.m.