Up: Component summary
Up: Component summary
Component
DiffMeth
Function to compute differential methylation at a base/window/region resolution. It uses functions contained in the R package methylKit.
| 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) ; data.table (R-package) ; download (bash) ; methylKit |
| Source files | component.xml DiffMeth.R |
| Usage | Example with default values |
| Deprecated |
This component is not part of the methylation pipeline anymore. |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| rawFilteredNormMethyl | BinaryFile | Mandatory | Binary file containing the RData output from MethFilterNorm |
| regions | BED | Optional | A 6 field BED file containing the locations and IDs of the regions where methylation has to be summarized. |
Outputs| Name | Type | Description |
|---|---|---|
| plots | Latex | Folder containing plots about correlation analysis, clustering and PCA. |
| differentialMethylation | BinaryFile | File containing the differential methylation information in RData format. This is the input file for the component SelectDiffMeth |
| visualization | BinaryFolder | Folder containing the bedgraph file used to visualize the differential methylation across the genome. |
| analysis | CSVList | Folder containing CSV files with methylation summarized by region/window and differential methylation information. |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| agglMethod | string | "ward" | Agglomeration method to be used for the clustering of samples. Possible values are "ward", "single", "complete", "average", "mcquitty", "median" and "centroid". |
| bedgraph | boolean | false | Boolean value indicating if a bedgraph file should be printed in the visualization folder. The scores are meth.diff. |
| correlation | string | "pearson" | Correlation coefficient (or covariance) to be computed when performing sample correlation. Possible values are "pearson", "kendall" and "spearman". |
| covBases | int | 0 | Minimum number of bases to be covered in a given window. |
| dataFrame | boolean | false | Boolean value indicating if CSV files summarizing the methylation information for every sample should be printed in the analysis folder. |
| destrand | boolean | false | Boolean paramenter. If TRUE consider only the strand specific methylated Cs. |
| distance | string | "correlation" | Distance method to be used for the clustering of samples. Possible values are "correlation", "euclidean", "maximum", "manhattan", "canberra", "binary" and "minkowski". |
| minPerGroup | int | (no default) | Integer value denoting the minimum number of samples per condition needed to cover a region/window/base. By default only regions/bases that are covered in all samples are
united as methylBase object, however by supplying an integer for this argument users can control how many samples needed to cover region/window/base to be united
as methylBase object. For example, if minPerGroup set to 2 and there are 3 samples per condition, the bases/window/regions that are covered in at least 2 samples
will be united and missing data for uncovered bases/regions will appear as NAs. |
| mode | string | "base" | Designates whether methylation information have to be analyzed at base-pair, window or regional resolution.
Possible values are base, window or region.
When mode == "window", it is possible to summarize the methylation in windows of specified length using the parameters winSize, stepSize and covBases.
When mode == "region", it is possible to summarize the methylation at specific regions using the parameters covBases and strand.
The input file regions must be given as input. |
| numCores | int | 1 | Integer value denoting how many cores should be used for differential methylation calculations. |
| regionName | string | "" | Name of the regions contained in the region file. No spaces nor commas are allowed in the string. |
| similarityAnalysis | boolean | true | Boolean value indicating if correlation analysis, clustering and PCA need to be performed to analyzed the similarities among samples. |
| slim | boolean | true | Boolean values stating how to perform the P-value adjustment. If TRUE(default) SLIM method will be used for P-value adjustment. If FALSE, p.adjust with method="BH" option will be used for P-value correction. |
| stepSize | int | 1000 | An integer for the step size of tiling windows, it must be less or equal to winSize. |
| weigthedMean | boolean | true | Boolean values stating if the mean methylation difference between groups has to be computed using read coverage as weights. |
| winSize | int | 1000 | An integer for the size of the tiling windows. It has to be an integer greater than 1. |
Test cases| Test case | Parameters▼ | IN rawFilteredNormMethyl |
IN regions |
OUT plots |
OUT differentialMethylation |
OUT visualization |
OUT analysis |
|---|---|---|---|---|---|---|---|
| case1_default | properties | rawFilteredNormMethyl | (missing) | plots | differentialMethylation | (missing) | (missing) |
|
# Testing DiffMeth component, |
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| case2_window | properties | rawFilteredNormMethyl | (missing) | plots | differentialMethylation | (missing) | (missing) |
|
# Testing DiffMeth component, |
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| case3_region | properties | rawFilteredNormMethyl | regions | (missing) | differentialMethylation | (missing) | (missing) |
|
# Testing DiffMeth component, |
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| case4_dataFrame_and_bedgraph | properties | rawFilteredNormMethyl | (missing) | plots | differentialMethylation | visualization | analysis |
|
# Testing DiffMeth component, |
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