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SelectDiffMeth

Function to select which bases/windows/regions are significantly differentially methylated. Also, a barplot and a karyogram plot showing the distribition of hyper- and hypo-methylated bases/windows/regions are producted.

Version 1.0
Bundle sequencing
Categories Analysis
Authors Chiara Facciotto (chiara.facciotto@helsinki.fi)
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Requires R ; GenomicRanges (R-bioconductor) ; genomation (R-bioconductor) ; data.table (R-package) ; download (ant) ; methylKit (R-package) ; installer (bash)
Source files component.xml SelectDiffMeth.R
Usage Example with default values
Deprecated

This component is not part of the methylation pipeline anymore.

Inputs

Name Type Mandatory Description
differentialMethylation BinaryFile Mandatory Binary file containing the RData output from DiffMeth.
features BED Optional 6 field BED file containing the region for the methylation annotation.

Outputs

Name Type Description
signifDiffMeth CSV CSV files containing the significantly differentially methylated regions/windows/cytosines.
plots Latex Folder containg plots showing the distribution of hypo- and hypermethylated regions in every chromosome.
annotation BinaryFolder Folder containing the annotation information.
visualization BinaryFolder Folder containing the bedgraph files to visualize the significantly differentially methylated regions/windows/cytosines.

Parameters

Name Type Default Description
destrand boolean false Boolean paramenter. If true consider only the strand specific methylated Cs.
diffMeth int 25 Cutoff for percent methylation difference between states (e.g. between test and control).
featureName string "" String stating the type of features contained in the features file. No spaces nor commas are allowed in the string.
flankSize int 0 Integer value indicating the number of basepairs for the flanking regions. Used (but not compulsory) when the file features is given.
qvalue float 0.01 Cutoff for qvalue of differential methylation statistic.

Test cases

Test case Parameters IN
differentialMethylation
IN
features
OUT
signifDiffMeth
OUT
plots
OUT
annotation
OUT
visualization
case1_default (missing) differentialMethylation (missing) signifDiffMeth plots (missing) visualization
case2_diffMeth_qvalue properties differentialMethylation (missing) signifDiffMeth plots (missing) visualization

# Testing SelectDiffMeth component,
diffMeth=15,
qvalue=0.05

case3_features properties differentialMethylation features signifDiffMeth plots annotation visualization

# Testing SelectDiffMeth component,
flankSize=5,
featureName=features


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