reporter_score: One step to get the reporter score of your KO abundance...

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

One step to get the reporter score of your KO abundance table.

Description

One step to get the reporter score of your KO abundance table.

Usage

reporter_score(
  kodf,
  group,
  metadata = NULL,
  method = "wilcox.test",
  pattern = NULL,
  p.adjust.method1 = "none",
  mode = c("directed", "mixed")[1],
  verbose = TRUE,
  feature = "ko",
  type = c("pathway", "module")[1],
  p.adjust.method2 = "BH",
  modulelist = NULL,
  threads = 1,
  perm = 4999,
  min_exist_KO = 3,
  max_exist_KO = 600
)

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
method	the type of test. Default is 'wilcox.test'. Allowed values include: t.test (parametric) and wilcox.test (non-parametric). Perform comparison between two groups of samples. If the grouping variable contains more than two levels, then a pairwise comparison is performed. anova (parametric) and kruskal.test (non-parametric). Perform one-way ANOVA test comparing multiple groups. 'pearson', 'kendall', or 'spearman' (correlation), see cor.
pattern	a named vector matching the group, e.g. c('G1'=1,'G2'=3,'G3'=2), use the correlation analysis with specific pattern to calculate p-value.
p.adjust.method1	p.adjust.method for 'ko.test', see p.adjust
mode	'mixed' or 'directed' (default, only for two groups differential analysis or multi-groups correlation analysis.), see details in pvalue2zs.
verbose	logical
feature	one of 'ko', 'gene', 'compound'
type	'pathway' or 'module' for default KOlist for microbiome, 'CC', 'MF', 'BP', 'ALL' for default GOlist for homo sapiens. And org in listed in 'https://www.genome.jp/kegg/catalog/org_list.html' such as 'hsa' (if your kodf is come from a specific organism, you should specify type here).
p.adjust.method2	p.adjust.method for the correction of ReporterScore, see p.adjust
modulelist	NULL or customized modulelist dataframe, must contain 'id','K_num','KOs','Description' columns. Take the 'KOlist' as example, use custom_modulelist.
threads	default 1
perm	permutation number, default: 4999.
min_exist_KO	min exist KO number in a pathway (default, 3, when a pathway contains KOs less than 3, there will be no RS)
max_exist_KO	max exist KO number in a pathway (default, 600, when a pathway contains KOs more than 600, there will be no RS)

Value

reporter_score object:

kodf	your input KO_abundance table
ko_stat	ko statistics result contains p.value and z_score
reporter_s	the reporter score in each pathway
modulelist	default KOlist or customized modulelist dataframe
group	The comparison groups in your data
metadata	sample information dataframe contains group

for the 'reporter_s' in result, whose columns represent:

ID	pathway id
Description	pathway description
K_num	total number of KOs/genes in the pathway
Exist_K_num	number of KOs/genes in your inputdata that exist in the pathway
Significant_K_num	number of kos/genes in your inputdata that are significant in the pathway
Z_score	Z_{pathway}=\frac{1}{\sqrt{k}}\sum Z_{koi}
BG_Mean	Background mean, \mu _k
BG_Sd	Background standard deviation, \sigma _k
ReporterScore	ReporterScore of the pathway, ReporterScore=(Z_{pathway}-\mu _k)/\sigma _k
p.value	p.value of the ReporterScore
p.adjust	adjusted p.value by p.adjust.method2

See Also

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

Examples

message("The following example require some time to run:")

data("KO_abundance_test")
reporter_score_res <- reporter_score(KO_abundance, "Group", metadata,
  mode = "directed", perm = 499
)
head(reporter_score_res$reporter_s)
reporter_score_res2 <- reporter_score(KO_abundance, "Group2", metadata,
  mode = "mixed",
  method = "kruskal.test", p.adjust.method1 = "none", perm = 499
)
reporter_score_res3 <- reporter_score(KO_abundance, "Group2", metadata,
  mode = "directed",
  method = "pearson", pattern = c("G1" = 1, "G2" = 3, "G3" = 2), perm = 499
)

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