Up: Component summary
Up: Component summary
Component
SelectDiffMethFunction 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 | DNA Methylation |
| Authors | Chiara Facciotto (chiara.facciotto@helsinki.fi) |
| Issue tracker | View/Report issues |
| 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 |
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# Testing SelectDiffMeth component, |
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| case3_features | properties | differentialMethylation | features | signifDiffMeth | plots | annotation | visualization |
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# Testing SelectDiffMeth component, |
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