Skip to content

Commit

Permalink
Browse files Browse the repository at this point in the history
Added new parameters to documentation
  • Loading branch information
jenzopr committed Jul 10, 2015
1 parent ff8c15d commit aa20511
Showing 1 changed file with 13 additions and 0 deletions.
13 changes: 13 additions & 0 deletions DOCUMENTATION.md
Expand Up @@ -28,6 +28,8 @@ ADMIRE was developed as an open source, semi-automatic analysis pipeline and vis
- Supports arbitrary number of samples and sample groups
- Differential methylation analysis on pre-calculated and individual genomic regions
- Provides ready-to-plug-in files for genome browsers (like IGV)
- Provides publication-ready figures for the most differentially methylated regions
- Performs gene set enrichment analysis on predefined and individual gene sets

### Workflow

Expand Down Expand Up @@ -60,6 +62,8 @@ Parameter | Explanation
-l | In case of quantile normalization, label samples as bad if their median signals are below a given value (10.5)
-m | In case of quantile normalization, remove bad samples
-q | Q-value cutoff for multiple testing correction (0.05)
-i | Render advanced plots for the best i regions (20)
-g | Gene set file for enrichment analysis, use multiple -g parameters to calculate enrichment over many gene sets
-o | tar-gz compress output into file given
-h | shows this help message
-v | shows version information
Expand Down Expand Up @@ -107,6 +111,10 @@ ADMIRE is also able to work on raw methylation values when called with `admire -
In case of functional normalization, an additional noob background correction step can be skipped with `admire -b -n fn`.
In case of functional or noob normalization, a dye correction step can be skipped with `ADMIRE -d -n fn` or `admire -d -n noob`.

#### Gene set enrichment analysis

Gene sets can be given with `admire -g geneset1 -g geneset2 ...`. Gene set files should be text files with one gene symbol per line. The filename is used to name the gene set.

#### Other available parameters

ADMIRE features the following other parameters:
Expand All @@ -126,6 +134,7 @@ This subdirectory contains a csv file for each combination of sample group compa
#### Files in the visualization subdirectory

This subdirectory contains files for visualization with IGV. General files, like the genomic location of all Illumina probes, as well as the genomics regions used during analysis, are located in the `annotation-tracks` subfolder. Data specific files are located in the `data-tracks` folder. Here, you can find information per sample-group comparison (e.g. case-vs-control) information on significantly altered probe methylation (`control-case.igv`), as well as significantly altered genomic regions in [BED format](http://genome.ucsc.edu/FAQ/FAQformat.html#format1).
Additionally, additional images are stored in region-specific subdirectories.

#### Files in the normalized subdirectory

Expand All @@ -135,6 +144,10 @@ When not using inside the galaxy environment, the `normalized` subdirectory cont

When not using inside the galaxy environment, the `results` subdirectory contains intermediate result files, like the output from statistical testing (`control-case.pvals.bed`) or results from combining p-values (`comb-p` subdirectory).

#### Files in the geneset-enrichment subdirectory

tba

### Examples

#### Detection of differentially methylated promoters in permanent atrial fibrillation
Expand Down

0 comments on commit aa20511

Please sign in to comment.