Up: Component summary
Up: Component summary
Component
PlinkWraps Plink software that allows various genome wide SNP data manipulations and analyzes. Some functions are predefined and can be run using functionType parameter. Also other commands can be executed. Many of the Plink text-format outputs are easily transformed into csv-format to be further used in the Anduril-workflow. Text2CSV-component in the Anduril beta-bundle can be used for the transformation.
| Version | 1.1 |
|---|---|
| Bundle | microarray |
| Categories | SNP |
| Authors | Sirkku Karinen (sirkku.karinen@helsinki.fi) |
| Issue tracker | View/Report issues |
| Requires | plink ; installer (bash) |
| Source files | component.xml |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| pedFile | TextFile | Mandatory | SNP-data in ped format. http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#ped |
| mapFile | TextFile | Optional | Map file for annotating SNPs in ped-file. If no map file is given, Plink uses map file that is in the same directory with ped file AND is named in the same fashion i.e. myPedFIle.ped and myPedFile.map. If binary files are in use, map file needs to be given in this way. |
| file1 | BinaryFile | Optional | Additional file that can be given to command is referred as @f1@ in the command |
| file2 | BinaryFile | Optional | Additional file that can be given to command is referred as @f2@ in the command |
| file3 | BinaryFile | Optional | Additional file that can be given to command is referred as @f3@ in the command |
Outputs| Name | Type | Description |
|---|---|---|
| result1 | TextFile | One of following predefined result files are put into this output port (if command is used): ld : plink.ld haploblock : plink.blocks hardy : plink.hwe |
| result2 | TextFile | One of following predefined result files are put into this output port (if command is used): haploblock : plink.blocks.det |
| result3 | TextFile | |
| result4 | TextFile | |
| result5 | TextFile |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| Plink | string | "/opt/share/plink/plink" | Path to Plink-program. This default is for CSBL old server. Gives Java IOException if this path not set correctly. |
| dataType | string | "text" | Type of the input ped file text/binary |
| functionType | string | (no default) | Plink command: ld : linkage (r2) calculation http://pngu.mgh.harvard.edu/~purcell/plink/ld.shtml#ld2 haploblock : haplotype block estimation http://pngu.mgh.harvard.edu/~purcell/plink/ld.shtml#blox hardy : calculation of Hardy-Weinberg statistics http://pngu.mgh.harvard.edu/~purcell/plink/thresh.shtml#hwd custom : parameters-parameter defines the Plink-command |
| outputFiles | string | "" | Comma separated list of filenames that (custom) Plink commad produces. (plink.ped, plink.map, plink.freq,....see manual) These files will be inserted into output ports (result1,2...5) in the same order as they are in this list. This parameter is not used in predefined analyzes (ld,haploblock,hardy...) |
| parameters | string | "" | Either additional parameters or full Plink command. EXAMPLES 1) Select samples and create new dataset. (use with parameter outputFiles="plink.ped,plink.map"): --keep /file/path/list_of_samples.csv --recode. 2) Calculate allele frequencies (use with parameter outputFiles="plink.frq") :--freq |
Test cases| Test case | Parameters▼ | IN pedFile |
IN mapFile |
IN file1 |
IN file2 |
IN file3 |
OUT result1 |
OUT result2 |
OUT result3 |
OUT result4 |
OUT result5 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| case1 | properties | pedFile | mapFile | (missing) | (missing) | (missing) | (missing) | result2 | result3 | result4 | result5 |
|
functionType = ld |
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| case2 | properties | pedFile | mapFile | (missing) | (missing) | (missing) | result1 | result2 | result3 | result4 | result5 |
|
functionType = hardy |
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| case3 | properties | pedFile | mapFile | (missing) | (missing) | (missing) | result1 | result2 | result3 | result4 | result5 |
|
functionType = custom, |
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