combine_rs_res: Combine the results of 'step by step GRSA'

In ReporterScore: Generalized Reporter Score-Based Enrichment Analysis for Omics Data

Combine the results of 'step by step GRSA'

Description

Combine the results of 'step by step GRSA'

Usage

combine_rs_res(kodf, group, metadata, ko_stat, reporter_s, modulelist = NULL)

Arguments

kodf	KO_abundance table, rowname are feature ids (e.g. K00001 if feature="ko"; PEX11A if feature="gene"; C00024 if feature="compound"), colnames are samples.
group	The comparison groups (at least two categories) in your data, one column name of metadata when metadata exist or a vector whose length equal to columns number of kodf. And you can use factor levels to change order.
metadata	sample information data.frame contains group
ko_stat	result of pvalue2zs
reporter_s	result of get_reporter_score
modulelist	NULL or customized modulelist dataframe, must contain 'id','K_num','KOs','Description' columns. Take the 'KOlist' as example, use custom_modulelist.

Value

reporter_score object

See Also

Other GRSA: get_reporter_score(), ko.test(), pvalue2zs(), reporter_score()

Examples

data("KO_abundance_test")
ko_pvalue <- ko.test(KO_abundance, "Group", metadata)
ko_stat <- pvalue2zs(ko_pvalue, mode = "directed")
reporter_s1 <- get_reporter_score(ko_stat, perm = 499)
reporter_res <- combine_rs_res(KO_abundance, "Group", metadata, ko_stat, reporter_s1)

ReporterScore documentation built on Sept. 11, 2024, 6:44 p.m.