averageIntensities: Average protein/peptide abundances for each condition studied

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

Average protein/peptide abundances for each condition studied

Description

Calculate the average of the abundances for each protein in each condition for an ExpressionSet or MSnSet. Needs to have the array expression data ordered in the same way as the phenotype data (columns of the array data in the same order than the condition column in the phenotype data).

Usage

averageIntensities(ESet_obj)

Arguments

ESet_obj

ExpressionSet object containing all the data

Value

a dataframe in wide format providing (in the case of 3 or more conditions) the means of intensities for each protein/peptide in each condition. If there are less than 3 conditions, an error message is returned.

Author(s)

Helene Borges

Examples

data(Exp1_R25_prot, package="DAPARdata")
obj <- Exp1_R25_prot[seq_len(1000)]
level <- 'protein'
metacell.mask <- match.metacell(GetMetacell(obj), c("Missing POV", "Missing MEC"), level)
indices <- GetIndices_WholeMatrix(metacell.mask, op = ">=", th = 1)
obj <- MetaCellFiltering(obj, indices, cmd = "delete")
averageIntensities(obj$new)

prostarproteomics/DAPAR documentation built on Oct. 11, 2024, 12:03 p.m.