match_prior_info: match_prior_info match the prior information to the given...

In mqzhanglab/wHC: Goodness of fit Statistics Calculation based on weighted p-values

match_prior_info match the prior information to the given gene set from collection of MSigDB

Description

match_prior_info match the prior information to the given gene set from collection of MSigDB

Usage

match_prior_info(net, prior_info, add_option = "none", report_option = TRUE)

Arguments

net	dataframe the gmt file from collections of Molecular signatures database (MSigDB), broad institute.
prior_info	the numeric vector representing prior information for each single gene, with genes name corresponding to that in the net.
add_option	defines the method of adding up missing values. It can be "none", "mean" or "median". No actions for adding up missing values if "none".
report_option	if TRUE, report current procedures of the path, which is the proportion of sets completed the matching steps.

Value

a dataframe with the same format as net,which is the gmt files

References

Liberzon, A., Subramanian, A., Pinchback, R., Thorvaldsdóttir, H., Tamayo, P., & Mesirov, J. P. (2011). Molecular signatures database (MSigDB) 3.0. Bioinformatics, 27(12), 1739–1740. https://doi.org/10.1093/bioinformatics/btr260

Examples

net=net.h.all.v6.1.symbols
#net from MSigDB (software.broadinstitute.org/gsea/msigdb): "h.all.v6.1.symbols.gmt"
prior_gi=get_genic_intolerance()
prior_net=match_prior_info(net,prior_gi)

mqzhanglab/wHC documentation built on April 1, 2022, 6:28 p.m.