Biowulf High Performance Computing at the NIH
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.


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


   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]

     Variance inactive component

     Variation tolerance

     Bound tolerance

     Eps node prior parameter b

     Eps node prior parameter a

     Alpha node prior parameter b

     Alpha node prior parameter a

   -i ,  --n_iter 
     Number of iterations

   -n ,  --n_factors 
     Number of hidden factors

     Factor prior file

   -c ,  --cov_file 
     Covariate data file

     Expression uncertainty (variance) data file

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

   -o ,  --out_dir 
     Output directory

     Expression and covariates files have a header

     Add a covariate to model mean effect

     No output of weight precision

     No output of posterior sparsity prior

     No output of estimated factor weights

     No output of estimated factors

     No output of residual values

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

     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 ~]$