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Description |
▸ FORGE2 is the new version of
FORGE, including new stats and multiple epigenetic datasets.
▸ FORGE2 identifies tissue- or cell type-specific signal by analysing a minimum set of 5 single nucleotide polymorphisms (SNPs) for overlap with epigenetic data peaks compared to matched background SNPs and provides both graphical and tabular outputs. ▸ FORGE2 incorporates data across DNase I hypersensitive sites (DHSs), histone mark chromatin immunoprecipitation (ChIP) broadpeaks, and hidden Markov model (HMM) chromatin states. |
Input data |
▸ Source You can upload a file, provide a URL for an existing file or simply copy-paste your data on the text box provided. ▸ Input file format If specified, specify the file format as follow: SNP list: list of SNPs as rsIDs each on a separate line. Optionally can add other fields after the rsID which are ignored, unless the p-value filter is specified, in which case FORGE2 assumes that the second field is the -log10 p-value. ▸ Platform Select which SNP array has been used to generate these data ("GWAS") ▸ Maximum number of probes The web version is limited to 1000 rsIDs. While it is possible to input a larger number of rsIDs with the standalone version, you must consider how the background selection occurs. |
Options |
▸ Name for this data Supply a label that you want to use for the plotting titles, and filenames. ▸ Analysis data from Dataset to analyse. Consolidated Roadmap Epigenomics DHS data is selected as the default. ▸ Depletion Analyse for depletion pattern instead of the default enrichment analysis. Use when dealing with SNP datasets suspected not to overlap with a certain epigenetic peak dataset. Specifying depletion will be indicated on the label (the text "Depletion Analysis" will be added to the file label). ▸ Proximity Apply a filter for SNPs in LD (LD < 0.8 with another test SNP). With LD filtering specified, FORGE2 will report SNPs removed due to LD with another SNP in the list and will pick only one SNP from the set of SNPs that are in LD. ▸ Background repetitions The number of background matching sets to pick and analyse. (1-1000) ▸ Significance threshold Alter the default binomial p-value thresholds. (0 < Strict < Marginal < 1) |
Output |
▸ Raw data A tab-separated values (tsv) file with columns for the Zscore, Pvalue, Cell, Tissue, File, rsID, Number and Accession. ▸ Static chart A PDF chart of the data. ▸ Interactive chart A dimple (http://dimplejs.org) d3 interactive graphic using rCharts. ▸ Interactive table A table using the Datatables (https://datatables.net) plug-in for the jQuery Javascript library, again accessed through rChartsA dimple (http://dimplejs.org) d3 interactive graphic using rCharts. ▸ R code The source files for generating the charts and the table. You can download the raw data and use R (http://www.r-project.org) with these file to re-generate or modify the output. |