Package: reconsi 1.19.0

Stijn Hawinkel

reconsi: Resampling Collapsed Null Distributions for Simultaneous Inference

Improves simultaneous inference under dependence of tests by estimating a collapsed null distribution through resampling. Accounting for the dependence between tests increases the power while reducing the variability of the false discovery proportion. This dependence is common in genomics applications, e.g. when combining flow cytometry measurements with microbiome sequence counts.

Authors:Stijn Hawinkel [cre, aut]

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NEWS

# Install 'reconsi' in R:

install.packages('reconsi', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/centerforstatistics-ugent/reconsi/issues

Datasets:

Vandeputte - Microbiomes of Crohn's disease patients and healthy controls

On BioConductor:reconsi-1.19.0(bioc 3.21)reconsi-1.18.0(bioc 3.20)

metagenomics microbiome multiplecomparison flowcytometry

4.60 score 2 stars 2 scripts 130 downloads 7 exports 83 dependencies

Last updated 25 days agofrom:ebca5ca16f. Checks:OK: 1 WARNING: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 17 2024
R-4.5-win	WARNING	Nov 17 2024
R-4.5-linux	WARNING	Nov 17 2024
R-4.4-win	WARNING	Nov 17 2024
R-4.4-mac	WARNING	Nov 17 2024
R-4.3-win	WARNING	Nov 17 2024
R-4.3-mac	WARNING	Nov 17 2024

Exports:getApproxCovar getC1prop plotApproxCovar plotCovar plotNull reconsi testDAA

Dependencies:ade4 ape askpass Biobase BiocGenerics biomformat Biostrings cli cluster codetools colorspace cpp11 crayon curl data.table digest fansi farver FNN foreach generics GenomeInfoDb GenomeInfoDbData ggplot2 glue gtable httr igraph IRanges isoband iterators jsonlite kernlab KernSmooth ks labeling lattice lifecycle magrittr MASS Matrix matrixStats mclust mgcv mime multicool multtest munsell mvtnorm nlme openssl permute phyloseq pillar pixmap pkgconfig plyr pracma R6 RColorBrewer Rcpp RcppArmadillo reshape2 rhdf5 rhdf5filters Rhdf5lib rlang S4Vectors scales sp stringi stringr survival sys tibble UCSC.utils utf8 vctrs vegan viridisLite withr XVector zlibbioc

Manual for the RCM pacakage

Rendered fromreconsiVignette.Rmdusingknitr::rmarkdownon Nov 17 2024.

Last update: 2023-11-10
Started: 2019-11-05

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Bin the test statistic into equally sized bins	binStats
Obtain weights as posterior probabilities to calculate the consensus null	calcWeights
Fast estimation of mean and standard deviation of a normal distrbution, optionally with weights	estNormal
Estimate the fraction of true null hypotheses.	estP0
Obtain a null covariance matrix of binned test statistics	getApproxCovar
Find the dependence pat C1 of the approximate covariance matrix, and extract the ratio of the first eigenvalue to the sum of all positive eigenvalues	getC1prop
Calculate tail-area (Fdr) and local (fdr) false discovery rates, based on a certain null distribution	getFdr
Obtain the consensus null	getG0
A function to calculate observed and permuation z-statistics on a n-by-p matrix of observations	getTestStats
A function to obtain a t-test statistic efficiently. For internal use only	getTstat
Plot an approximation of the correlation structure of the test statistics	plotApproxCovar
Plot an the corvariance matrix of the test statistics estimated through permutations	plotCovar
Plot the obtained null distribution along with a histogram of observed test statistics	plotNull
A custom function to calculate the distribution function of the t-test statistic. For internal use only	ptEdit
A custom function to calculate the quantile function of the t-test statistic. For internal use only	qtEdit
Correct quantiles by not returning 0 or 1	quantCorrect
Perform simultaneous inference through collapsed resampling null distributions	reconsi
A function to efficiently row multiply a a-by-b matrix by a vector of length b. More memory intensive but that does not matter with given matrix sizes	rowMultiply
A function to numerically stabilize an exponentiation. For internal use only	stabExp
A function to test for differential absolute abundance on a phyloseq object	testDAA testDAA,matrix-method testDAA,phyloseq-method
Microbiomes of Crohn's disease patients and healthy controls	Vandeputte