farmsSummary: 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 factor analysis

Usage

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farmsSummary(dat,group_col=2)

Arguments

dat

an data frame with raw peptide or psm intensities

group_col

the column by which peptides/psm intensity are grouped. Usually it is the gene/protein id 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"]]
# farms method does not tolerate missing values
dat.gene = farmsSummary(dat.psm,group_col=2) 

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