Description Usage Arguments Value
Second 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; (b) first order PC if they only connect to one shared genes and (c) second order PC by removing the controls pair by pair if they connect
to more than two shared neighbours genes. After that, the fdrtool
is used to calculate the p-value, FDR and connection probability from the correlation.
1 2 |
data.exp |
gene expression data matrix with genes in columns and samples in rows. |
edgelist |
an edge list for second 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 |
method |
estimators of correlation. Options are "pearson", "spearman" and "kendall". |
logical. |
If TRUE, a progressbar will show to indicate the code runing percentage. |
secondPC
returns a data frame with columns of regulators, target genes, edge correlation weigthes, p-values, FRD and connection probability.
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