PWcTalkNWpre: Cascaded steps in pathway crosstalk analyis prior to network...
In Haocan223/MetaGSCA: Meta Gene Set Co-expression Analysis

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/PWcTalkNWpre.R

Identify crosstalk pathway pairs from pathway-wise statistical significance values (p-values) across multiple datasets.

1	PWcTalkNWpre(input2PWcTalk,test=c('binary','binary')[1],pTh.dataset,pTh.pwPair,pTh.pw)

`input2PWcTalk`	Input CSV file name or a data frame object. The matrix within the file or the data frame must contain gene set analysis results (p-values) across multiple datasets, as well as a bootstrap.p column which represents the meta-analysis result.
`test`	The test method used to quantify pathway similarity between two binary vectors. Default is binary.
`pTh.dataset`	P-values in the pathway-by-dataset matrix less than pTh.dataset are converted to 1 and those greater than the threshold are converted to 0.
`pTh.pwPair`	Pathway pairs with similarity value (p-value or an analogy) less than pTh.pwPair are retained as edges of the graph of pathway crosstalk.
`pTh.pw`	Pathways with meta-analysis p-value less than pTh.pw are retained as vertices of the graph of pathway crosstalk.

PWcTalkNWpre first infers pathway pairwise similarity from a dichotomized pathway-by-dataset p-value matrix, then apply an edge filter and a node filter to obtain a network of discrete pathway connections.

Firstly, the algorithm converts the pathway-dataset p-value matrix to a binary matrix on account of pTh.dataset. Then, it quantifies similarity between all possible pathway pairs using either the asymmetric binary similarity (the binary method of R function dist) or Pearson's phi (enabled through R function crosstable_statistics from R package sjstats). If test is set as phi, the pairwise distance value is inverted to a similarity metric through 1-dist operation and converted to percentages in a high-to-low sorted list. Finally, a graph (network) is defined by retaining pathway connections with similarity measure lower than pTh.pwPair, provided that the involved pathways have their meta-analysis p-value less than pTh.pw. If pTh.pw is set to 1, the vertex filter is waived.

a list object with two components:

`g`	A graph object as defined in R package igraph.
`tkid`	The identifier of the current tkplot window. This should be supplied to function tk_coords once layout adjustment is completed.

Hui Yu schena.yu@gmail.com

PWcTalkNW

data(input2PWcTalk)
## One code block to execute pathway crosstalk analysis. More code lines, but enabling interactive layout tuning.
preNW <- PWcTalkNWpre(input2PWcTalk,test='binary',
  pTh.dataset=0.01,pTh.pwPair=0.01,pTh.pw=0.01)
g_tkid <- PWcTalkNW(preNW$PW.pair,preNW$PW.p)
##### PAUSE here: adjust the network layout on the pop-out window to reach a satisfaction #####
coords <- tk_coords(g_tkid$tkid)
g_tkid <- PWcTalkNW(preNW$PW.pair,preNW$PW.p,layout=coords,pdfW=14,pdfH=10,figname='PWcTalk',asp=0.5)