countPeptides: Count the number of peptides in each group

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

Count the number of peptides in each group

Description

Given a protdata object, a dataframe pData containing experiment information and a predictor of interest, returns a data frame giving the amount of peptides observed for each level of the predictor.

Usage

countPeptides(protdata, pData, predictor)

Arguments

protdata	A protdata object
pData	A dataframe that contains experimenter-supplied variables describing phenotypes and/or experimental factors that might influence the quantitative value of interest for each mass spec run. The colnames should be all the different effects that influence the outcome. The first column should hold all the different run names. The corresponding levels of the other effects should be in the subsequent columns.
predictor	A predictor for which you would like to summarize the number of identified peptides per level for each protein. This predictor should correspond to one element of the colnames of pData.

statOmics/MSqRob documentation built on Dec. 8, 2022, 6 a.m.