Combine the results of 'step by step GRSA'

Combine the results of 'step by step GRSA'

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

# \donttest{
data("KO_abundance_test")
ko_pvalue <- ko.test(KO_abundance, "Group", metadata)
#> =================================Checking group=================================
#> 30 samples are matched for next step.
#> ===========================Removing all-zero rows: 0============================
#> ==============================Calculating each KO===============================
#> ===========================Using method: wilcox.test============================
#> 1000 features done.
#> 2000 features done.
#> 3000 features done.
#> 4000 features done.
#> 
#> Compared groups: WT, OE
#> Total KO number: 4535
#> Compare method: wilcox.test
#> Time use: 3.273
ko_stat <- pvalue2zs(ko_pvalue, mode = "directed")
reporter_s1 <- get_reporter_score(ko_stat, perm = 499)
#> ================================Use feature: ko=================================
#> ===============================Checking rownames================================
#> Some of your ko_stat are not KO id, check the format! (e.g. K00001)
#> 52.7% of your kos in the modulelist!
#> ==================================load KOlist===================================
#> ================KOlist download time: 2023-07-28 06:07:08.466916================
#> If you want to update KOlist, use `update_KO_file()`
#> ============================Calculating each pathway============================
#> 100 pathways done.
#> 400 pathways done.
#> ID number: 481
#> Time use: 2.187
reporter_res <- combine_rs_res(KO_abundance, "Group", metadata, ko_stat, reporter_s1)
# }