This mode is used to combine tab delimited output files and adjust P-values for multiple testing. It is implemented by
edu.cornell.med.icb.goby.modes.FalseDiscoveryRateMode.java. The tool is efficient in that it only keeps P-values that need to be adjusted in memory, but otherwise keeps other column on disk. This strategy is expected to scale to hundreds of millions of lines of information. Since Goby 1.9.
Mode Parameters
The following options are available in this mode
| Flag | Arguments | Required | Description |
|---|---|---|---|
n/a | input | yes | Tab delimited files to append and perform FDR adjustment on. |
(-o|--output) | output | yes | The file where the combined output will be written. If the filename ends in .gz, the output is compressed with gzip. |
(-q|--q-threshold) | q-threshold | no | Threshold on the q-value for a line to be written to the output. If any of the adjusted P-value is below this threshold, the line is written to the output. Default value: 1.0 |
(-c|--column) | column | no | Name of a column containing a P-value to adjust. |
--vcf | n/a | no | When this switch is provided, input are read in the Variant Call Format (VCF) and output produced in VCF. Default value: FALSE |
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