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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:

• Oliver Stegle, Leopold Parts, Richard Durbin, and John Winn
  A Bayesian Framework to Account for Complex Non-Genetic Factors in Gene Expression Levels Greatly Increases Power in eQTL Studies
  PLoS Computational Biology 2010, 6(5), e1000770. doi:10.1371/journal.pcbi.1000770
  
• Leopold Parts, Oliver Stegle, John Winn, and Richard Durbin
  Joint Genetic Analysis of Gene Expression Data with Inferred Cellular Phenotypes
  PLoS Genetics 2011, 7(1), e1001276. doi:10.1371/journal.pgen.1001276

• PEER Tutorial on GitHub

• Module Name: PEER (see the modules page for more information)
• Unusual environment variables set
  • PEER_HOME  PEER installation directory
  • PEER_BIN       PEER executable directory
  • PEER_DOC       PEER documentation directory
  • PEER_DATA    PEER test data directory

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 ~]$