firstPC: First order partial correlation

In wyguo/RLowPCor: Inference of co-expression gene network using relevance low order partial correlation from large scale expression data

Description

First order PC is calcuated according to the edge connections in the input edgelist. The correlation of a pair of genes are calcuated as (a) correlation if they do not connect to the same neighbour genes and (b) the maximum of first order PC values by removing the controls one by one if they connect to shared neighbour genes. After that, the cor2statistics is used to calculate the p-value, FDR and connection probability from the output correlation.

Usage

firstPC(data.exp, edgelist, controlist = NULL, method = "pearson",
  progressbar = T)

Arguments

data.exp	gene expression data matrix with genes in columns and samples in rows.
edgelist	an edge list for fisrt order PC calculation. The PC values are calcuated over each pair of genes in the gene list.
controlist	list of vectors of neighbour genes for each pair of genes in edgelist. The vector order in the list must match to the order of corresponding paired genes in the input edgelist. For example the i element in controlist contains the shared neighbours of gene edgelist[i,1] and gene edgelist[i,2].
method	estimators of correlation. Options are "pearson", "spearman" and "kendall".
logical.	If TRUE, a progressbar will show to indicate the code runing percentage.

Value

firstPC returns a data frame with columns of regulators, target genes, edge correlation weigthes, p-values, FRD and connection probability.

See Also

cor2statistics, RLowPC

wyguo/RLowPCor documentation built on May 4, 2019, 12:04 p.m.