medianSweeping: summarize peptide/PSM intensity into protein level relative...

In yafeng/DEqMS: a tool to perform statistical analysis of differential protein expression for quantitative proteomics data.

summarize peptide/PSM intensity into protein level relative abundance estimate by median sweeping method

Description

This function is to calculate proteins'relative abundance by median sweeping method

Usage

medianSweeping(dat,group_col=2)

Arguments

dat	an data frame with peptide/PSM intensities in log2 scale
group_col	the column by which peptides/PSM intensity are grouped. Usually the gene/protein id column. Default is 2

Value

a data frame with protein relative abundance estimate in log2 scale

Author(s)

Yafeng Zhu

Examples

library(ExperimentHub)
eh = ExperimentHub(localHub=TRUE)
query(eh, "DEqMS")
dat.psm = eh[["EH1663"]]

dat.psm.log = dat.psm
dat.psm.log[,3:12] =  log2(dat.psm[,3:12])

dat.gene.nm = medianSweeping(dat.psm.log,group_col = 2)

yafeng/DEqMS documentation built on Nov. 29, 2024, 1:48 a.m.