PWcTalk: Streamlined functions for Pathway Crosstalk Network analysis

In hui-sheen/MetaGSCA: Meta-analysis of Gene Set differential Co-expression Analysis

Streamlined functions for Pathway Crosstalk Network analysis

Description

Overall main function packed as a cascade of major sub-functions

Usage

PWcTalk(
  input2PWcTalk,
  test = "binary",
  pTh.dataset = 0.01,
  pTh.pwPair = 0.01,
  pTh.pw = 0.01,
  figname = "PWcTalk",
  pdfW = 10,
  pdfH = 10,
  asp = 0.7,
  vbase = 15,
  ebase = 2,
  vlbase = 1,
  power = 1/2
)

Arguments

input2PWcTalk	A data frame with 330 observations across 14 variables. Each observation corresponds to a pathway
test	Similarity measure over two binary vectors, either asymmetric Binary similarity or Pearson's Phi index
pTh.dataset	Threshold for permutation p-statistic of a gene set co-expression in a dataset
pTh.pwPair	Threshold for the similarity measure between two pathways
pTh.pw	Threshold for the meta-analysis p-statistic of a pathway’s co-expression across multiple datasets
figname	Stem file name for the resultant pathway crosstalk network figure
pdfW	Width of PDF figure file
pdfH	Height of PDF figure file
asp	Aspect ratio (between width and height). Asp parameter of function plot.igraph
vbase	A base value regarding vertex size. Vertex size depends on vbase and a soft thresholding Power parameter
ebase	A base value regarding edge width. Edge width depends on ebase and a soft thresholding Power parameter
vlbase	A base value regarding verbex label. Vertex label font depends on vlbase and a soft thresholding Power parameter
power	A power paramter involved in soft-thresholding treatment. Power is implicated in vertex size, edge width, and vertex label font

Details

Nevertheless, it is recommended to collapse the function and run the sub-functions in a script instead.

Value

An igraph graph (network) object

See Also

[PWcTalkNWpre()] for the first module of prior steps, [PWcTalkNW()] for the second module of post steps.

Other aggregations: PWcTalkNWpre(), PWcTalkNW()

Examples

data(input2PWcTalk)
#Execute pathway crosstalk analysis in one command. 
#Code requires XMing support (x11 server), thus being turned off.
#PWcTalk(input2PWcTalk,test='binary',
# pTh.dataset=0.01,pTh.pwPair=0.01,pTh.pw=0.01,figname='PWcTalk',
# pdfW=10,pdfH=10,asp=0.7,vbase=15,ebase=2,vlbase=1,power=1/2)

hui-sheen/MetaGSCA documentation built on April 9, 2022, 7:24 p.m.