computeT2: Compute T^2 and its p-value for each pathway

In roqe/T2GA: Pathway Analysis Tools for Quantitative Proteomic Data

Description

This function computes the T^2 score and its significance level.

Usage

computeT2(
  data,
  purb = 1.5,
  pathDB = "KEGG",
  ppi = STRING_v11,
  intg = TRUE,
  alpha = 0.05,
  ncore = 1
)

Arguments

data	Processed data using importdata function.
purb	Perturbance threshold, default is 1.5 (after normalization).
pathDB	Pathway database: "KEGG" or "Reactome".
ppi	Protein-protein interaction database: "STRING_ppi" or "HitPredict_ppi".
intg	Apply pathway integration or not, default is TRUE.
alpha	Significance level, default is 0.05.
ncore	Number of parallel computing cores, default is 1.

Examples

dat1=importdata(TCR_5min)
res1=computeT2(dat1)
dat2=importdata(TCR_5min,TCR_15min)
res2=computeT2(dat2,pathDB="Reactome",ppi=HitPredict_v4)

roqe/T2GA documentation built on March 9, 2021, 9:38 p.m.