medianSummary: 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 taking the median

Description

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

Usage

medianSummary(dat,group_col=2,ref_col)

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
ref_col	an integer vector indicating the column(s) used as denominator to calcualte relative petide ratio.

Value

a data frame containing 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])
# use the 3 ctrl samples as reference channels to calculate log2 ratio
dat.gene = medianSummary(dat.psm.log,group_col = 2,ref_col =c(3,7,10))

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