pvalue2zs: Transfer p-value of KOs to Z-score

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

Transfer p-value of KOs to Z-score

Description

Transfer p-value of KOs to Z-score

Usage

pvalue2zs(
  ko_pvalue,
  mode = c("directed", "mixed")[1],
  p.adjust.method1 = "none"
)

Arguments

ko_pvalue	data.frame from ko.test, 'KO_id' and 'p.value' columns are required.
mode	'mixed' or 'directed' (default, only for two groups differential analysis or multi-groups correlation analysis.), see details in pvalue2zs.
p.adjust.method1	p.adjust.method for 'ko.test', see p.adjust

Details

'mixed' mode is the original reporter-score method from Patil, K. R. et al. PNAS 2005. In this mode, the reporter score is undirected, and the larger the reporter score, the more significant the enrichment, but it cannot indicate the up-and-down regulation information of the pathway! (Liu, L. et al. iMeta 2023.)

steps:

1. Use the Wilcoxon rank sum test to obtain the P value of the significance of each KO difference between the two groups (ie P_{koi}, i represents a certain KO);

2. Using an inverse normal distribution, convert the P value of each KO into a Z value (Z_{koi}), the formula:

Z_{koi}=\theta ^{-1}(1-P_{koi})

3. 'Upgrade' KO to pathway: Z_{koi}, calculate the Z value of the pathway, the formula:

Z_{pathway}=\frac{1}{\sqrt{k}}\sum Z_{koi}

where k means A total of k KOs were annotated to the corresponding pathway;

4. Evaluate the degree of significance: permutation (permutation) 1000 times, get the random distribution of Z_{pathway}, the formula:

Z_{adjustedpathway}=(Z_{pathway}-\mu _k)/\sigma _k

\mu _k is The mean of the random distribution, \sigma _k is the standard deviation of the random distribution.

Instead, 'directed' mode is a derived version of 'mixed', referenced from https://github.com/wangpeng407/ReporterScore.

This approach is based on the same assumption of many differential analysis methods: the expression of most genes has no significant change.

steps:

1. Use the Wilcoxon rank sum test to obtain the P value of the significance of each KO difference between the two groups (ie P_{koi}, i represents a certain KO), and then divide the P value by 2, that is, the range of (0,1] becomes (0,0.5], P_{koi}=P_{koi}/2;

2. Using an inverse normal distribution, convert the P value of each KO into a Z value (Z_{koi}), the formula:

Z_{koi}=\theta ^{-1}(1-P_{koi})

since the above P value is less than 0.5, all Z values will be greater than 0;

3. Considering whether each KO is up-regulated or down-regulated, calculate diff\_KO,

Z_{koi}=-Z_{koi}\ \ \ \ (diff\_KO<0),

so Z_{koi} is greater than 0 Up-regulation, Z_{koi} less than 0 is down-regulation;

4. 'Upgrade' KO to pathway: Z_{koi}, calculate the Z value of the pathway, the formula:

Z_{pathway}=\frac{1}{\sqrt{k}}\sum Z_{koi}

where k means A total of k KOs were annotated to the corresponding pathway;

5. Evaluate the degree of significance: permutation (permutation) 1000 times, get the random distribution of Z_{pathway}, the formula:

Z_{adjustedpathway}=(Z_{pathway}-\mu _k)/\sigma _k

\mu _k is The mean of the random distribution, \sigma _k is the standard deviation of the random distribution.

The finally obtained Z_{adjustedpathway} is the Reporter score value enriched for each pathway. In this mode, the Reporter score is directed, and a larger positive value represents a significant up-regulation enrichment, and a smaller negative values represent significant down-regulation enrichment.

However, the disadvantage of this mode is that when a pathway contains about the same number of significantly up-regulates KOs and significantly down-regulates KOs, the final absolute value of Reporter score may approach 0, becoming a pathway that has not been significantly enriched.

Value

ko_stat data.frame

References

1. Patil, K. R. & Nielsen, J. Uncovering transcriptional regulation of metabolism by using metabolic network topology. Proc Natl Acad Sci U S A 102, 2685–2689 (2005). 2. Liu, L., Zhu, R. & Wu, D. Misuse of reporter score in microbial enrichment analysis. iMeta n/a, e95. 3. https://github.com/wangpeng407/ReporterScore

See Also

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

Examples

data("KO_abundance_test")
ko_pvalue <- ko.test(KO_abundance, "Group", metadata)
ko_stat <- pvalue2zs(ko_pvalue, mode = "directed")

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