LFQ: LFQ workflow

Description Usage Arguments Value Examples

View source: R/workflow_functions.R

Description

LFQ is a wrapper function running the entire differential enrichment/expression analysis workflow for label free quantification (LFQ)-based proteomics data. The protein table from MaxQuant is used as direct input.

Usage

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LFQ(proteins, expdesign, fun = c("man", "bpca", "knn", "QRILC", "MLE",
  "MinDet", "MinProb", "min", "zero", "mixed", "nbavg"), type = c("all",
  "control", "manual"), control = NULL, test = NULL,
  filter = c("Reverse", "Potential.contaminant"), name = "Gene.names",
  ids = "Protein.IDs", alpha = 0.05, lfc = 1)

Arguments

proteins

Data.frame, The data object.

expdesign

Data.frame, The experimental design object.

fun

"man", "bpca", "knn", "QRILC", "MLE", "MinDet", "MinProb", "min", "zero", "mixed" or "nbavg", Function used for data imputation based on manual_impute and impute.

type

'all', 'control' or 'manual', The type of contrasts that will be generated.

control

Character(1), The sample name to which the contrasts are generated (the control sample would be most appropriate).

test

Character, The contrasts that will be tested if type = "manual". These should be formatted as "SampleA_vs_SampleB" or c("SampleA_vs_SampleC", "SampleB_vs_SampleC").

filter

Character, Name(s) of the column(s) to be filtered on.

name

Character(1), Name of the column representing gene names.

ids

'Character(1), Name of the column representing protein IDs.

alpha

Numeric(1), sets the false discovery rate threshold.

lfc

Numeric(1), sets the log fold change threshold.

Value

A list of 9 objects:

data

data.frame containing the original data

se

SummarizedExperiment object containing the original data

filt

SummarizedExperiment object containing the filtered data

norm

SummarizedExperiment object containing the normalized data

imputed

SummarizedExperiment object containing the imputed data

diff

SummarizedExperiment object containing FDR estimates of differential expression

dep

SummarizedExperiment object annotated with logical columns indicating significant proteins

results

data.frame containing containing all results variables from the performed analysis

param

data.frame containing the test parameters

Examples

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data <- UbiLength
expdesign <- UbiLength_ExpDesign
results <- LFQ(data, expdesign, 'MinProb', 'control', 'Ctrl')

arnesmits/DEP documentation built on Aug. 7, 2019, 10:44 a.m.