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PEER: probabilistic estimation of expression residuals

PEER stands for "probabilistic estimation of expression residuals". It is a collection of Bayesian approaches to infer hidden determinants and their effects from gene expression profiles using factor analysis methods.

References:

Documentation
Important Notes

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive 
[user@cn3107 ~]$module load PEER
[user@cn3107 ~]$peertool --help

USAGE: 

   peertool  [--sigma_off ] [--var_tol ] [--bound_tol
             ] [--e_pb ] [--e_pa ] [--a_pb ]
             [--a_pa ] [-i ] [-n ] [--prior ] [-c
             ] [--var_file ] -f  [-o ]
             [--has_header] [--add_mean] [--no_a_out] [--no_z_out]
             [--no_w_out] [--no_x_out] [--no_res_out] [--] [--version]
             [-h]
Where: 

   --sigma_off 
     Variance inactive component

   --var_tol 
     Variation tolerance

   --bound_tol 
     Bound tolerance

   --e_pb 
     Eps node prior parameter b

   --e_pa 
     Eps node prior parameter a

   --a_pb 
     Alpha node prior parameter b

   --a_pa 
     Alpha node prior parameter a

   -i ,  --n_iter 
     Number of iterations

   -n ,  --n_factors 
     Number of hidden factors

   --prior 
     Factor prior file

   -c ,  --cov_file 
     Covariate data file

   --var_file 
     Expression uncertainty (variance) data file

   -f ,  --file 
     (required)  Expression data file

   -o ,  --out_dir 
     Output directory

   --has_header
     Expression and covariates files have a header

   --add_mean
     Add a covariate to model mean effect

   --no_a_out
     No output of weight precision

   --no_z_out
     No output of posterior sparsity prior

   --no_w_out
     No output of estimated factor weights

   --no_x_out
     No output of estimated factors

   --no_res_out
     No output of residual values

   --,  --ignore_rest
     Ignores the rest of the labeled arguments following this flag.

   --version
     Displays version information and exits.

   -h,  --help
     Displays usage information and exits.

   Probabilistic estimation of expression residuals (PEER)

[user@cn3107 ~]$cp $PEER_DATA/* . 
[user@cn3107 ~]$cd peer/examples/data
Basic usage:
[user@cn3107 ~]$peertool -f expression.csv -n 
	iteration 0/50
	iteration 1/50
	iteration 2/50
	iteration 3/50
	iteration 4/50
Converged (var(residuals)) after 4 iterations
If there are measured experimental variables that may contribute to variability in the data, they can be included in the inference, and specified with the -c flag.
[user@cn3107 ~]$peertool -f expression_sparse.csv -c covs.csv --out_dir expression_sparse_out
	iteration 0/50
	iteration 1/50
	iteration 2/50
	iteration 3/50
	iteration 4/50
	iteration 5/50
	iteration 6/50
	iteration 7/50
	iteration 8/50
Converged (var(residuals)) after 8 iterations

End the interactive session:
[user@cn3107 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$