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

Description Usage Arguments Value Author(s) Examples

View source: R/DEqMS.R

Description

This function is to calculate proteins'relative abundance by Turkey median polish

Usage

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medpolishSummary(dat,group_col=2)

Arguments

dat

an data frame containing peptide/psm intensities in log2 scale

group_col

the column by which peptides/psm intensity are grouped. Usually the gene/protein column. Default is 2

Value

a data frame containing protein relative abundance estimate in log2 scale

Author(s)

Yafeng Zhu

Examples

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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 = medpolishSummary(dat.psm.log,group_col=2)

DEqMS documentation built on Nov. 8, 2020, 7:51 p.m.