Combp is a library to combine, analyze, group and correct p-values in BED files. Unique tools involve correction for spatial autocorrelation. This is useful for ChIP-Seq probes and Tiling arrays, or any data with spatial correlation.

References:

• Pedersen BS, Schwartz DA, Yang IV, Kechris KJ. Comb-p: software for combining, analyzing, grouping and correcting spatially correlated P-values. Bioinformatics. 2012 Nov 15;28(22):2986-8. doi: 10.1093/bioinformatics/bts545. Epub 2012 Sep 5. PubMed |  Journal

• combp Main Site:Main Site

• Module Name: combp (see the modules page for more information)

  	comb-p --help

• Environment variables set
  • $COMBP_TESTDATA

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive --cpus-per-task=2 --mem=2G
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load combp
[user@cn3144 ~]$ comb-p
Tools for viewing and adjusting p-values in BED files.

   Contact: Brent Pedersen - bpederse@gmail.com
   License: BSD

To run, indicate one of:

   acf       - calculate autocorrelation within BED file
   slk       - Stouffer-Liptak-Kechris correction of correlated p-values
   fdr       - Benjamini-Hochberg correction of p-values
   peaks     - find peaks in a BED file.
   region_p  - generate SLK p-values for a region (of p-values)
   filter    - filter region_p output on size and p and add coef/t
   hist      - plot a histogram of a column and check for uniformity.
   manhattan - a manhattan plot of values in a BED file.
   pipeline  - run acf, slk, fdr, peaks, region_p in succesion

NOTE: most of these assume *sorted* BED files.
SEE: https://github.com/brentp/combined-pvalues for documentation

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. combp.sh). For example:

#!/bin/bash
#SBATCH --cpus-per-task=2
#SBATCH --mem=2G
#SBATCH --time=2:00:00
#SBATCH --partition=norm

set -e
module load combp
cp $COMBP_TESTDATA/pvals.bed .
comb-p acf -d 1:500:50 -c 5 pvals.bed > acf.txt

Submit the job:

sbatch combp.sh

Create a swarmfile (e.g. job.swarm). For example:

       cd dir1; comb-p peaks --seed 0.05 --dist 1000 pvals1.bed >pvals.peaks1.bed
       cd dir2; comb-p peaks --seed 0.05 --dist 1000 pvals2.bed >pvals.peaks2.bed

    

Submit this job using the swarm command.

swarm -f job.swarm [-g #] --module combp