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A pipeline that enables pre-processing of 450k data, a selection of normalization methods and novel methods for downstream analysis including Probe Lasso DMR Hunter and Copy Number Alteration analysis.
● Data Source:
BioConductor
● Keywords: 450k, Beadchip, DNAMethylation, Epic, HumanMethylation450, array, methylation, package
● Alias: ChAMP, ChAMP-package
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This function enables CNA profiles to be built using methylation data from Illumina HumanMethylation450 BeadChips.
● Data Source:
BioConductor
● Keywords: copynumber
● Alias: champ.CNA
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Applying Bumphunter or ProbeLasso Algorithms to Estimate regions for which a genomic profile deviates from its baseline value. Originally implemented to detect differentially methylated genomic regions between two populations. By default, we recommend user do champ.DMR on normalized beta value on two populations, like case to control. The function will return detected DMR and estimated p value. The two algorithms specified in this function is different, while Bumphunter calcuated averaged candidate bumps methylation value between case and control, ProbeLasso need Different Methylated Probes (DMP) from champ.MVP as input parameter and find DMRs around those DMPs. Thus parameters is different for two algorithms.
● Data Source:
BioConductor
● Keywords: Bumphunter, DMR, ProbeLasso
● Alias: champ.DMR
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This function
● Data Source:
BioConductor
● Keywords: limma
● Alias: champ.MVP
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Runs Singular Value Decomposition on a dataset to estimate the impact of batch effects.
● Data Source:
BioConductor
● Keywords: batch effects
● Alias: champ.SVD
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This function
● Data Source:
BioConductor
● Keywords: limma
● Alias: champ.TrueMethyl
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Function that loads data from IDAT files to calculate intensity and produce quality control images.
● Data Source:
BioConductor
● Keywords:
● Alias: champ.load
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Option to normalize data with a selection of normalization methods.
● Data Source:
BioConductor
● Keywords: normalization
● Alias: champ.norm
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This function allows the user to run the entire pipeline in one function. Arguments allow user to select functions if desired.
● Data Source:
BioConductor
● Keywords: 450K data
● Alias: champ.process
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Applying References-Based Methold to correct cell-proportion in a methylation dataset. Reference-based method use purified whole blood cell-type specific methylation value to correct beta value dataset. Cell Proportions for each cell-type will be detected, and lm function will be used to correct beta value for 5 largest cell types. Cell type with smallest cell proportion will not be corrected.
● Data Source:
BioConductor
● Keywords: celltype
● Alias: champ.refbase
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