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Chromosome-level genome assembly of the nematophagous flatworm Luticola nematophagus: revealing molecular adaptations for predation and its biocontrol potential against nematode diseases.

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Paper

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The authors' code

R · 91 lines · 3.6 KB · no license

  1. #' @title Calculate p-values from a set of observed test statistics and
  2. #' simulated null test statistics
  3. #'
  4. #' @description Calculates p-values from a set of observed test statistics and
  5. #' simulated null test statistics
  6. #'
  7. #' @param stat A vector of calculated test statistics.
  8. #' @param stat0 A vector or matrix of simulated or data-resampled null test
  9. #' statistics.
  10. #' @param pool If FALSE, stat0 must be a matrix with the number of rows equal to
  11. #' the length of \code{stat}. Default is TRUE.
  12. #'
  13. #' @details The argument \code{stat} must be such that the larger the value is
  14. #' the more deviated (i.e., "more extreme") from the null hypothesis it is.
  15. #' Examples include an F-statistic or the absolute value of a t-statistic. The
  16. #' argument \code{stat0} should be calculated analogously on data that
  17. #' represents observations from the null hypothesis distribution. The p-values
  18. #' are calculated as the proportion of values from \code{stat0} that are
  19. #' greater than or equal to that from \code{stat}. If \code{pool=TRUE} is
  20. #' selected, then all of \code{stat0} is used in calculating the p-value for a
  21. #' given entry of \code{stat}. If \code{pool=FALSE}, then it is assumed that
  22. #' \code{stat0} is a matrix, where \code{stat0[i,]} is used to calculate the
  23. #' p-value for \code{stat[i]}. The function \code{empPvals} calculates
  24. #' "pooled" p-values faster than using a for-loop.
  25. #'
  26. #' See page 18 of the Supporting Information in Storey et al. (2005) PNAS
  27. #' (\url{http://www.pnas.org/content/suppl/2005/08/26/0504609102.DC1/04609SuppAppendix.pdf})
  28. #' for an explanation as to why calculating p-values from pooled empirical
  29. #' null statistics and then estimating FDR on these p-values is equivalent to
  30. #' directly thresholding the test statistics themselves and utilizing an
  31. #' analogous FDR estimator.
  32. #'
  33. #' @return A vector of p-values calculated as described above.
  34. #'
  35. #' @references Storey JD and Tibshirani R. (2003) Statistical significance for
  36. #' genome-wide experiments. Proceedings of the National Academy of Sciences,
  37. #' 100: 9440-9445. \cr \url{http://www.pnas.org/content/100/16/9440.full}
  38. #'
  39. #' Storey JD, Xiao W, Leek JT, Tompkins RG, Davis RW. (2005) Significance
  40. #' analysis of time course microarray experiments. Proceedings of the
  41. #' National Academy of Sciences, 102 (36), 12837-12842. \cr
  42. #' \url{http://www.pnas.org/content/102/36/12837.full.pdf?with-ds=yes}
  43. #'
  44. #' @examples
  45. #' # import data
  46. #' data(hedenfalk)
  47. #' stat <- hedenfalk$stat
  48. #' stat0 <- hedenfalk$stat0 #vector from null distribution
  49. #'
  50. #' # calculate p-values
  51. #' p.pooled <- empPvals(stat=stat, stat0=stat0)
  52. #' p.testspecific <- empPvals(stat=stat, stat0=stat0, pool=FALSE)
  53. #'
  54. #' # compare pooled to test-specific p-values
  55. #' qqplot(p.pooled, p.testspecific); abline(0,1)
  56. #'
  57. #' @author John D. Storey
  58. #' @seealso \code{\link{qvalue}}
  59. #' @aliases empPvals
  60. #' @keywords pvalues
  61. #' @export
  62. empPvals <- function(stat, stat0, pool = TRUE) {
  63. m <- length(stat)
  64. n <- ncol(stat0)
  65. # Calculates p-values
  66. if (pool == TRUE) {
  67. if (is.matrix(stat0)) {
  68. stat0 <- as.vector(stat0)
  69. }
  70. m0 <- length(stat0)
  71. v <- c(rep(TRUE, m), rep(FALSE, m0))
  72. v <- v[order(c(stat, stat0), decreasing = TRUE)]
  73. u <- 1:length(v)
  74. w <- 1:m
  75. p <- (u[v == TRUE] - w) / m0
  76. p <- p[rank(-stat)]
  77. p <- pmax(p, 1/m0)
  78. } else {
  79. if (is.vector(stat0)) {
  80. stop("stat0 must be a matrix.")
  81. } else if (n == m) {
  82. stat0 <- t(stat0)
  83. } else if (nrow(stat0) != m){
  84. stop("Number of rows of stat0 must equal length of stat.")
  85. }
  86. stat0 <- (stat0 - stat) >= 0
  87. p <- rowMeans(stat0)
  88. p <- pmax(p, 1 / ncol(stat0))
  89. }
  90. return(p)
  91. }

empPvals.R at commit e861423, no license · at the source

Overview

Authors: Chongtao Guo1,2,3, Wang Yin1,2,3,4, Zhouqiong Zhang1,2,3, Renju Deng1,2,3, Shouhui Pan5, Hai Zhang5, Hao Cen5, Quan Zhang5, Fei Dai5, Congyong Li5, Qing Yang5
  1. Biotechnology Institute of Guizhou Province, Guiyang, Guizhou China
  2. Guizhou Key Laboratory of Agricultural Biotechnology, Guiyang, Guizhou China
  3. Ministry of Agriculture and Rural Affairs Key Laboratory of Crop Genetic Resources and Germplasm Innovation in Karst Region, Guiyang, Guizhou China
  4. Guizhou Zhikang Biotechnology Company, Guizhou, China
  5. Anshun Branch of Guizhou Tobacco Company, Anshun, Guizhou China
Institutions: Ministry of Agriculture and Rural Affairs (China)
Journal: BMC genomics, volume 27, issue 1, article 523
Dates: received 26 November 2025; accepted 13 April 2026; published online 23 April 2026
Type: Research article · Language: English
License: CC BY-NC-ND
Identifiers: DOI 10.1186/s12864-026-12863-z · PMID 42021141 · PMCID PMC13238120 · OpenAlex W7155223899
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: other (organism), cellular / molecular (subfield)
Methods: Statistics
Keywords: Luticola nematophagus, Rhabdocoela, Chromosome-level genome assembly, Nematode predation, Biocontrol, Comparative genomics
MeSH: Chromosomes*, Genome, Helminth*, Genomics*, Platyhelminths*, Adaptation, Physiological, Animals, Nematoda, Pest Control, Biological (* major topic)
Topic: Planarian Biology and Electrostimulation (Molecular Biology, Biochemistry, Genetics and Molecular Biology), according to OpenAlex
Funding: Guizhou Provincial Science and Technology Projects (QKHJC-[2024]youth076); Youth Fund (Natural Science) Project of Guizhou Academy of Agricultural Sciences ([2024]04); major Scientific and Technological Project of the Anshun Branch of Guizhou Tobacco Company (2023ASXM04)
Citations: not cited yet (Europe PMC); 106 references in the paper

Abstract

The abstract is not reproduced here: the paper's license (CC BY-NC-ND) does not allow it. Read it in the paper, at the publisher or on Europe PMC.

Repository

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StoreyLab/qvalue

License: none: the authors keep all their rights
State: the link answers, verified on 29 September 2026
Evidence: files inventoried
Commit: e8614232f05dd3db0951fafe3b2a33b8284b2aff, 1 September 2023
Languages: R (11)
Size: 27 files, 11 scripts
Software Heritage: not archived
Found in: the text, “Gene family expansion and contraction analysis”
Holds: README, environment (DESCRIPTION), documentation
Not found: license file, CITATION.cff, tests, continuous integration
Availability: 1 check, the latest on 29 September 2026: the link answers
  • 29 September 2026: the link answers
12 files
At the source: github.com/StoreyLab/qvalue

Code availability statement

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  • no repository, dataset or request procedure was recognized in it

Read it in the paper: doi.org/10.1186/s12864-026-12863-z.

Tracing map

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What the map holds:

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  • 11 scripts, each with its path and the digest of its content;
  • no match between paragraphs and code yet;
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Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.

Data

Datasets cited

Data availability statement

The paper has a data availability statement. Its license (CC BY-NC-ND) does not allow reproducing it here; in short, from what the harvester recognized in it:

Read it in the paper: doi.org/10.1186/s12864-026-12863-z.

Versions

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Version 1, 29 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 11 authors, 6 keywords, 8 MeSH terms, 3 funders, 106 references.

Cite

This paper

Guo, C., Yin, W., Zhang, Z., Deng, R., Pan, S., Zhang, H., Cen, H., Zhang, Q., Dai, F., Li, C., & Yang, Q. (2026). Chromosome-level genome assembly of the nematophagous flatworm Luticola nematophagus: revealing molecular adaptations for predation and its biocontrol potential against nematode diseases. BMC genomics, 27(1), 523. https://doi.org/10.1186/s12864-026-12863-z

BibTeX

@article{guo2026chromosome,
author = {Guo, Chongtao and Yin, Wang and Zhang, Zhouqiong and Deng, Renju and Pan, Shouhui and Zhang, Hai and Cen, Hao and Zhang, Quan and Dai, Fei and Li, Congyong and Yang, Qing},
title = {{Chromosome-level genome assembly of the nematophagous flatworm Luticola nematophagus: revealing molecular adaptations for predation and its biocontrol potential against nematode diseases}},
journal = {BMC genomics},
year = {2026},
month = apr,
volume = {27},
number = {1},
pages = {523},
publisher = {BMC},
issn = {1471-2164},
doi = {10.1186/s12864-026-12863-z},
url = {https://doi.org/10.1186/s12864-026-12863-z},
pmid = {42021141},
pmcid = {PMC13238120}
}

RIS

TY - JOUR
AU - Guo, Chongtao
AU - Yin, Wang
AU - Zhang, Zhouqiong
AU - Deng, Renju
AU - Pan, Shouhui
AU - Zhang, Hai
AU - Cen, Hao
AU - Zhang, Quan
AU - Dai, Fei
AU - Li, Congyong
AU - Yang, Qing
TI - Chromosome-level genome assembly of the nematophagous flatworm Luticola nematophagus: revealing molecular adaptations for predation and its biocontrol potential against nematode diseases
T2 - BMC genomics
J2 - BMC Genomics
PY - 2026
DA - 2026/04/23
VL - 27
IS - 1
SP - 523
SN - 1471-2164
PB - BMC
DO - 10.1186/s12864-026-12863-z
UR - https://doi.org/10.1186/s12864-026-12863-z
LA - en
ER -

CSL-JSON

{
"id": "10.1186/s12864-026-12863-z",
"type": "article-journal",
"title": "Chromosome-level genome assembly of the nematophagous flatworm Luticola nematophagus: revealing molecular adaptations for predation and its biocontrol potential against nematode diseases",
"container-title": "BMC genomics",
"author": [
{
"family": "Guo",
"given": "Chongtao"
},
{
"family": "Yin",
"given": "Wang"
},
{
"family": "Zhang",
"given": "Zhouqiong"
},
{
"family": "Deng",
"given": "Renju"
},
{
"family": "Pan",
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},
{
"family": "Zhang",
"given": "Hai"
},
{
"family": "Cen",
"given": "Hao"
},
{
"family": "Zhang",
"given": "Quan"
},
{
"family": "Dai",
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},
{
"family": "Li",
"given": "Congyong"
},
{
"family": "Yang",
"given": "Qing"
}
],
"container-title-short": "BMC Genomics",
"volume": "27",
"issue": "1",
"page": "523",
"DOI": "10.1186/s12864-026-12863-z",
"PMID": "42021141",
"PMCID": "PMC13238120",
"ISSN": "1471-2164",
"publisher": "BMC",
"URL": "https://doi.org/10.1186/s12864-026-12863-z",
"language": "en",
"issued": {
"date-parts": [
[
2026,
4,
23
]
]
}
}

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