bumphunter protocols

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chevron_left Differentially methylated region detection Differentially methylated region detection chevron_right
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bumphunter specifications

Information


Unique identifier OMICS_19199
Name bumphunter
Software type Framework/Library, Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Artistic License version 2.0
Computer skills Advanced
Version 1.22.0
Stability Stable
Requirements
AnnotationDbi, limma, methods, stats, parallel, BiocGenerics, GenomicRanges, utils, testthat, GenomeInfoDb, locfit, RUnit, S4Vectors(>=0.9.25), GenomicFeatures, foreach, matrixStats, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, doParallel, IRanges(>=2.3.23), R(>=3.4), iterators, doRNG
Maintained Yes

Versioning


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Documentation


Maintainer


  • person_outline Rafael A. Irizarry <>

Additional information


http://bioconductor.org/packages/release/bioc/manuals/bumphunter/man/bumphunter.pdf

Publication for bumphunter

bumphunter in pipelines

 (5)
2018
PMCID: 5824607
PMID: 29484035
DOI: 10.1186/s13148-018-0457-4

[…] methylation analysis was performed using the remove unwanted variation (ruvm) method, taking twin pairing into account in order to identify cp-specific differentially methylated probes (dmps), and bumphunter was performed to identify differentially methylated regions (dmrs)., we identified 33 top-ranked dmps based on a nominal p value cut-off of p < 1 × 10−4 and two dmrs (p < 1 × 10−3) […]

2018
PMCID: 5876118
PMID: 29287311
DOI: 10.1002/art.40408

[…] small . per the regression model, p values were adjusted using the bonferroni correction for 428,232 tests., analysis of differentially methylated regions (dmrs) was performed as implemented in the bumphunter r package . coefficients from the above regression models were smoothed over genomic distance, generating candidate regions of differentially methylated cpg sites. statistical significance […]

2018
PMCID: 5904983
PMID: 29692867
DOI: 10.1186/s13148-018-0490-3

[…] p values were determined according to the method of benjamin and hochberg’s (bh method) multiple testing procedure []., differentially methylated regions (dmrs) were identified using the “bumphunter” method implemented in the “champ” r package with the parameters (b = 1000, useweights = true, minprobes = 10, pickcutoff = true, and other settings with default values) []., […]

2016
PMCID: 4767228
PMID: 26913521
DOI: 10.1371/journal.pgen.1005819

[…] the dnam levels of each probe, preserving the effect of fibroblast sampling location. finding differentially methylated regions (dmrs) involves identifying contiguous probes where β ≠ 0 using the bumphunter bioconductor package (version 1.6.0) [], here requiring |β| > 0.1 (argument: cutoff = 0.1) and assessing statistical significance using linear modeling bootstrapping with 1000 […]

2016
PMCID: 5399044
PMID: 27838757
DOI: 10.1007/s00204-016-1879-4

[…] methylated regions (dmrs), we first calculated a difference in methylation (∆meth) for each cpg position between high- and low-exposure groups. the function “regionfinder” was used in the bumphunter package version 1.2.0 [modified from a previously published method (jaffe et al. )], providing the locations of the clusters and using a cutoff of ∆meth = 10%. the dmrs were then filtered […]


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bumphunter in publications

 (43)
PMCID: 5925605
PMID: 29740534
DOI: 10.3389/fonc.2018.00100

[…] network hotspots composed of at least ten genes and fdr < 0.01 were reported., to identify genomic regions harboring methylation changes (dmrs), a bump-hunting approach was used by the bumphunter package (). the analysis considered regions with >20% change in the overall methylation between tumor and normal samples with gaps no more than 500 bp among neighboring cpgs. […]

PMCID: 5904983
PMID: 29692867
DOI: 10.1186/s13148-018-0490-3

[…] p values were determined according to the method of benjamin and hochberg’s (bh method) multiple testing procedure []., differentially methylated regions (dmrs) were identified using the “bumphunter” method implemented in the “champ” r package with the parameters (b = 1000, useweights = true, minprobes = 10, pickcutoff = true, and other settings with default values) []., […]

PMCID: 5902304
PMID: 29449426
DOI: 10.1183/13993003.01068-2017

[…] signalling by notch in severe asthma asmcs., we used a different approach to examine the importance of severity associated dmps, namely weighted gene co-expression analysis (wgcna) [] and bumphunter analysis []. we identified five out of 19 modules as being significantly correlated with disease severity (). filtering of these phenotype-associated cpg sites for significance […]

PMCID: 5877863
PMID: 29601581
DOI: 10.1371/journal.pone.0194938

[…] gran. both models were applied in the differentially methylated probes (dmps) analysis using the lmfit function (method = robust) and in differentially methylated regions (dmrs) analysis using the “bumphunter” function. dmp and dmr outcomes were used in all further evaluations. general methylation differences were evaluated by counting the probes with a δ < 0, representing hypomethylation […]

PMCID: 5870497
PMID: 29580210
DOI: 10.1186/s12864-018-4594-0

[…] at the regional level, we implemented a pipeline for the identification of differentially methylated regions (dmrs). raw p-values for individual cpg sites within each region designated by the bumphunter package were combined using the comb-p software [] and regional p-values were corrected for multiple testing. the comb-p package first calculates the correlation between proximal p-values […]


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bumphunter institution(s)
Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA; Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health. Baltimore, MD, USA; Center for Epigenetics, Johns Hopkins School of Medicine, Baltimore, MD, USA; Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
bumphunter funding source(s)
Partially supported by the National Institute of Health (grant numbers R01 GM083084, R01 RR021967, P50 HG003233; R01ES017646).

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