lfqevalupart: Conduct LFQ and assess performance of one specific LFQ...

In JianboFu0406/EVALFQ111: R Package for Evaluating Label-Free Proteome Quantification

Description

The ProteoLFQ enables the label-free quantification of proteomic data and the performance assessment of each LFQ workflow from multiple perspectives. This tool function gives the results based on each LFQ workflow and the criteria preferred and selected by the users. For function definitions and descriptions please use "??ProteoLFQ" command in R.

Usage

lfqevalupart(data_q, selectFile, Ca = "1", Cb = "1", Cc = "1", Cd = "1")

Arguments

data_q	This input file should be numeric type except the first and second column containing the names and label (control or case) of the studied samples, respectively. The intensity data should be provided in this input file with the following order: samples in row and proteins/peptides in column. Missing value (NA) of protein intensity are allowed.
selectFile	Input the name of your prefered strategies. Sample data of this data type is in the working directory (in github) “idrblab/EVALFQ/data/selectworkflows.rda”.
Ca	Criterion (a): precision of LFQ based on the proteomes among replicates (Proteomics. 15:3140-51, 2015). If set 1, the user chooses to assess LFQ workflows using Criterion (a). If set 0, the user excludes Criterion (a) from performance assessment. The default setting of this value is “1”.
Cb	Criterion (b): classification ability of LFQ between distinct sample groups (Nat Biotechnol. 28:83-9, 2010). If set 1, the user chooses to assess LFQ workflows using Criterion (b). If set 0, the user excludes Criterion (b) from performance assessment. The default setting of this value is “1”.
Cc	Criterion (c): differential expression analysis by reproducibility-optimization (Nat Biotechnol. 32:896-902, 2014). If set 1, the user chooses to assess LFQ workflows using Criterion (c). If set 0, the user excludes Criterion (c) from performance assessment. The default setting of this value is “1”.
Cd	Criterion (d): reproducibility of the identified protein markers among different datasets (Mol Biosyst. 11:1235-40, 2015). If set 1, the user chooses to assess LFQ workflows using Criterion (d). If set 0, the user excludes Criterion (d) from performance assessment. The default setting of this value is “1”.

Value

preprocessed matrix

Examples

wf <- lfqevalupart(data_q=my_df, selectFile=selectworkflows, Ca="1", Cb="1", Cc="1", Cd="1")

JianboFu0406/EVALFQ111 documentation built on Aug. 10, 2020, 1:49 p.m.