This is a package for the discovery of regulatory regions from Bis-seq data
● Data Source:
BioConductor
● Keywords: package
● Alias: MethylSeekR, MethylSeekR-package
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This function calculates the false discovery rate (FDR) based on randomized Bis-seq data.
● Data Source:
BioConductor
● Keywords:
● Alias: calculateFDRs
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0 images
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This function calculates the alpha values for a selected chromosome and plots the distribution of alpha values. The shape of the distribution is indicative of the presence or absence of partially methylated domains (PMDs).
● Data Source:
BioConductor
● Keywords:
● Alias: plotAlphaDistributionOneChr
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1 images
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This function plots the final segmentations, including PMDs, UMRs and LMRs.
● Data Source:
BioConductor
● Keywords:
● Alias: plotFinalSegmentation
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2 images
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This function generates a figure showing the PMD segmentation in a randomly chosen region.
● Data Source:
BioConductor
● Keywords:
● Alias: plotPMDSegmentation
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2 images
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Loading Bis-seq data from tab-delimited file or saved GRanges object
● Data Source:
BioConductor
● Keywords:
● Alias: readMethylome
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0 images
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Loading SNPs from tab-delimited file or saved GRanges object
● Data Source:
BioConductor
● Keywords:
● Alias: readSNPTable
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0 images
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Removes CpGs that overlap with SNPs from methylation GRanges object.
● Data Source:
BioConductor
● Keywords:
● Alias: removeSNPs
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0 images
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Save PMD segments in rds format and as tab-delimited file.
● Data Source:
BioConductor
● Keywords:
● Alias: savePMDSegments
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1 images
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Save UMR and LMRs segments in rds format and/or as tab-delimited file
● Data Source:
BioConductor
● Keywords:
● Alias: saveUMRLMRSegments
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1 images
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