The miner3-mechinf tool¶
This utility computes the mechanistic inference.
You can see the tool’s available options when you enter miner2-mechinf -h
at the command prompt:
usage: miner3-mechinf [-h] [-mc MINCORR]
expfile mapfile coexprdict outdir
miner3-mechinf - MINER compute mechanistic inference
positional arguments:
expfile input matrix
mapfile identifier mapping file
coexprdict coexpressionDictionary.json file from miner-coexpr
outdir output directory
optional arguments:
-h, --help show this help message and exit
--skip_tpm skip TPM preprocessing for single cell data
--tfs2genes FILE override TF to genes mapping (pickle or JSON file)
-mc MINCORR, --mincorr MINCORR
minimum correlation
Parameters in detail¶
miner3-mechinf
expects at least these 5 arguments:
expfile: The gene expression file a matrix in csv format.
mapfile: The gene identifier map file.
coexprdict: The path coexpressionDictionary.json file from the miner-coexpr tool
outdir: The path to the output directory
In addition, you can specify the following optional arguments:
--skip_tpm
: to skip the TPM preprocessing step for single-cell data
--tfs2genes
: provide alternative TF to genes mapping for computation
--mincorr
or--mc
: the minimum correlation value.
Output in detail¶
After successful completion there will be the following files in the output directory
regulons.json
- use this file in subsequent tools
coexpressionDictionary_annotated.json
mechanisticOutput.json
coexpressionModules_annotated.json
regulons_annotated.csv
coexpressionModules.json
regulons_annotated.json
coregulationModules.json