CpGassoc protocols

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CpGassoc specifications

Information


Unique identifier OMICS_00793
Name CpGassoc
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 2.60
Stability Stable
Requirements
qvalue, methods, R(≥2.10), nlme
Maintained Yes

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Maintainer


  • person_outline Richard T. Barfield <>

Publication for CpGassoc

CpGassoc in pipelines

 (5)
2017
PMCID: 5566454
PMID: 28827734
DOI: 10.1038/s41598-017-09335-6

[…] and qced using champ; the probe beta values were quantile-normalized using the ‘dasen’ method from the watermelon package. differential methylation on 425,694 probes post-qc was tested using the cpgassoc package, applying a linear model for tissue status at each probe, with individual id as covariate., following previous analyses, differentially methylated regions (dmrs) were defined […]

2016
PMCID: 4923870
PMID: 27349168
DOI: 10.1038/srep28657

[…] both reduced the genomic inflation factor to 1.2 and left 457 significantly associated cpgs at a fdr of 0.05 or less. the smartsva method was therefore used in subsequent analyses. the r package cpgassoc (rrid:scr_000320) was used to analyse differential methylation at single cpg sites where the results from the modified sva analysis were included as a covariate. the cpg.assoc function […]

2016
PMCID: 5005524
PMID: 27610375
DOI: 10.1155/2016/4369431

[…] 0.05 was used as the cut-off criterion. then, the methylation sites located in sex chromosomes were removed. finally, the associations between the screened methylation sites and lac were analyzed by cpgassoc package [] in r. the p value < 0.05 was taken as the threshold., according to the annotation information of the dna methylation profiles, the nearest genes to the lac-associated […]

2015
PMCID: 4588582
PMID: 26419812
DOI: 10.1038/srep14540

[…] procedure. statistical significance of the differentially methylated cpgs was determined using the fdr with a cut-off of 0.05 to correct for multiple hypothesis testing. running parallel to the cpgassoc method, a linear modelling using the limma package in rnbeads was used for computing the cpgs site specific p-values, with a fdr cut-off of 0.05., eligible pregnant women in early labour […]

2014
PMCID: 3915234
PMID: 24485148
DOI: 10.1186/1868-7083-6-4

[…] and 65 never smokers) was 90.72% at p = 1.1 × 10-7., all analyses were conducted in r, version 3.0.0 (http://www.r-project.org). the following packages were utilised: base, stats, lumi methylumi, cpgassoc, sva and randomforest [-]., mqtl: methylation quantitative trait locus; sabre: southall and brent revisited; snp: single nucleotide polymorphism., the authors declare […]

CpGassoc in publications

 (18)
PMCID: 5928241
PMID: 29712937
DOI: 10.1038/s41598-018-24755-8

[…] all samples from a given exposure experiment were processed in parallel and on parallel chips with replicate samples randomized with respect to chip position., a linear mixed effects model, cpgassoc, was used to perform quality control and to identify dna methylation changes significantly associated with dose, or with time after exposure. the 56fe ion, 28si ion, and x ray exposed […]

PMCID: 5738217
PMID: 29258561
DOI: 10.1186/s13104-017-3082-y

[…] ones containing snps at the investigated cpg site or at a single base extension position. probes located on the sex chromosomes were also excluded. the minfi preprocessed data were analyzed with the cpgassoc package to assess correlation of dna methylation profiles with complex posttraumatic symptoms measured by the tsi scales []. age, gender, the estimated proportion of buccal epithelial cells, […]

PMCID: 5730612
PMID: 29242640
DOI: 10.1038/s41598-017-18034-1

[…] these were filtered out. in addition, probes having a detection p-value above 0.01 were filtered out, and 1921 probes were thus removed from analysis. the remaining 483591 probes were analysed. the cpgassoc r package and methlab software were used for differential methylation analysis together with the humanmethylation450 v1.2 manifest file containing cpg annotations. t-statistics […]

PMCID: 5640901
PMID: 29046734
DOI: 10.1186/s13148-017-0414-7

[…] 13 mp2 [] to determine associations between cell types that were most likely to have a strong effect on results when adjusted for in ewas models., ewas were carried out in r version 3.0.2. using the cpgassoc package [] to model either asthma/wheeze status as the exposure and methylation (beta value) at either 7.5 or 16.5 years of age as the outcome. in addition to the cross-sectional ewas, […]

PMCID: 5566454
PMID: 28827734
DOI: 10.1038/s41598-017-09335-6

[…] and qced using champ; the probe beta values were quantile-normalized using the ‘dasen’ method from the watermelon package. differential methylation on 425,694 probes post-qc was tested using the cpgassoc package, applying a linear model for tissue status at each probe, with individual id as covariate., following previous analyses, differentially methylated regions (dmrs) were defined […]

CpGassoc institution(s)
Department of Bioinformatics and Biostatistics, School of Public Health, Emory University at Atlanta, GA, USA

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