The miner2-coexpr tool¶
This utility generates revised coexpression clusters from a gene expression file.
You can see the tool’s available options when you enter miner2-coexpr -h
at the command prompt:
usage: miner2-coexpr [-h] [-mg MINGENES] [-moxs MINOVEREXPSAMP]
[-mx MAXEXCLUSION] [-rs RANDSTATE] [-oxt OVEREXPTHRESH]
expfile mapfile outdir
miner2-coexpr - MINER cluster expression data.
positional arguments:
expfile input matrix
mapfile identifier mapping file
outdir output directory
optional arguments:
-h, --help show this help message and exit
-mg MINGENES, --mingenes MINGENES
min number genes
-moxs MINOVEREXPSAMP, --minoverexpsamp MINOVEREXPSAMP
minimum overexpression samples
-mx MAXEXCLUSION, --maxexclusion MAXEXCLUSION
maximum samples excluded
-rs RANDSTATE, --randstate RANDSTATE
random state
-oxt OVEREXPTHRESH, --overexpthresh OVEREXPTHRESH
overexpression threshold
Parameters in detail¶
miner2-coexpr
expects at least these 3 arguments:
expfile: The gene expression file a matrix in csv format.
mapfile: The gene identifier map file.
outdir: The path to the output directory
In addition, you can specify the following optional arguments:
--mingenes
or--mg
: the minimum number of genes in a cluster.
--minoverexpsamp
or--moxs
: minimum number of overexpression samples
--maxexclusion
or-mx
: maximum exclusion
--randstate
or-rs
: random state
--overexpthresh
or-oxt
: overexpression threshold
Output in detail¶
After successful completion there will be the following files in the output directory
cluster_size_distribution.pdf
: a plot of the cluster size distribution for visual verification
coexpressionDictionary.json
: this file is used in subsequent stages