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Usage: GRNBoost [infer] [options]
-h | --help
Prints this usage text.
-v | --version
Prints the version number.
Command: infer [options]
-i <file> | --input <file>
REQUIRED. Input file or directory.
-o <file> | --output <file>
REQUIRED. Output directory.
-tf <file> | --regulators <file>
REQUIRED. Text file containing the regulators (transcription factors), one regulator per line.
-skip <nr> | --skip-headers <nr>
The number of input file header lines to skip. Default: 0.
--delimiter <del>
The delimiter to use in input and output files. Default: TAB.
-s <nr> | --sample <nr>
Use a sample of size <nr> of the observations to infer the GRN.
--targets <gene1,gene2,gene3...>
List of genes for which to infer the putative regulators.
-p:<key>=<value> | --xgb-param:<key>=<value>
Add or overwrite an XGBoost booster parameter. Default parameters are:
* eta -> 0.01
* max_depth -> 1
* nthread -> 1
* silent -> 1
-r <nr> | --nr-boosting-rounds <nr>
Set the number of boosting rounds. Default: heuristically determined nr of boosting rounds.
--estimation-genes <gene1,gene2,gene3...>
List of genes to use for estimating the nr of boosting rounds.
--nr-estimation-genes <nr>
Nr of randomly selected genes to use for estimating the nr of boosting rounds. Default: 20.
--regularized
Enable regularization (using the triangle method). Default: disabled
When enabled, only regulations approved by the triangle method will be emitted.
When disabled, all regulations will be emitted.
Use the 'include-flags' option to specify whether to output the include flags in the result list.
--normalized
Enable normalization by dividing the gain scores of the regulations per target over the sum of gain scores.
Default = disabled.
--include-flags <true/false>
Flag whether to output the regularization include flags in the output. Default: false.
--truncate <nr>
Only keep the specified number regulations with highest importance score. Default: unlimited.
(Motivated by the 100.000 regulations limit for the DREAM challenges.)
-par <nr> | --nr-partitions <nr>
The number of Spark partitions used to infer the GRN. Default: nr of available processors.
--dry-run
Inference nor auto-config will launch if this flag is set. Use for parameters inspection.
--cfg-run
Auto-config will launch, inference will not if this flag is set. Use for config testing.
--report <true/false>
Set whether to write a report about the inference run to file. Default: true.