PEGASAS is a computational framework for pathway enrichment-guided activity study of alternative splicing. It correlates transcriptional signatures of 50 different cancer driver pathways with alternative splicing events.

References:

• John W. Phillipsa, Yang Panb, Brandon L. Tsaia, Zhijie Xiea, Levon Demirdjianc, Wen Xiaoa, Harry T. Yangb, Yida Zhangb, Chia Ho Lina, Donghui Chenga, Qiang Hud, Song Liud, Douglas L. Blacka, Owen N. Wittea, and Yi Xinga
  Pathway-guided analysis identifies Myc-dependent alternative pre-mRNA splicing in aggressive prostate cancers
  PNAS March 10, 2020, vol. 117, no. 10, 5269–5279
Documentation
• PEGASAS Github page
Important Notes
• Module Name: PEGASAS (see the modules page for more information)
• Unusual environment variables set
  • PEGASAS_HOME  installation directory
Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.



[user@biowulf]$ sinteractive --gres=gpu:v100:1 
[user@cn0861 ~]$ module load pegasas 
[+] Loading singularity  3.8.5-1  on cn4198 
[+] Loading pegasas 1.1.0  ...

[user@cn0861 ~]$ PEGASAS -h 
usage: PEGASAS [-h] [--version] {pathway,correlation} ...

PEGASAS -- PEGASAS

positional arguments:
  {pathway,correlation}
    pathway             Calculates signaling pathway activity derived from
                        geneset enrichment metric based on RNA-Seq gene
                        expression
    correlation         Computes pathway correlated alternative splicing
                        events

optional arguments:
  -h, --help            show this help message and exit
  --version             show program's version number and exit

For command line options of each sub-command, type: PEGASAS COMMAND -h

[user@cn0861 ~]$ PEGASAS pathway -h 
usage: PEGASAS pathway [-h] [-o OUT_DIR] [-n NUM_INTERVAL] [--plotting]
                       geneExpbySample geneSignatureList groupInfo

required arguments:
  geneExpbySample       A TSV format matrix of gene expression values (FPKM,
                        TPM, etc.) where each row is one sample and each
                        column is one gene.
  geneSignatureList     One or multiple gene signature sets of pathway of
                        interest in the format of 'gmt' (see MSigDB webset).
  groupInfo             A TSV format file provides patient ID and
                        phenotype/disease stage in each row.

optional arguments:
  -h, --help            show this help message and exit
  -o OUT_DIR, --out-dir OUT_DIR
                        Output folder name of the analysis.
  -n NUM_INTERVAL, --num-interval NUM_INTERVAL
                        Number of KS enrichment calculation processes one
                        time.
  --plotting            Making plots to inspect K-S enrichment scores.
[user@cn0861 ~]$ PEGASAS correlation -h 
usage: PEGASAS correlation [-h] [-o OUT_DIR] [--GO] [--GO-only]
                           [-b GO_BACKGROUND_GENE_LIST]
                           [--GOdb-versions GODB_VERSIONS]
                           signatureScorebySample PSIbySample groupNameOrder

required arguments:
  signatureScorebySample
                        A TSV format list of gene signature score where each
                        column is one sample and the corresponding score.
  PSIbySample           A TSV format matrix of PSI values where each column is
                        one sample and each row is one splicing event.
  groupNameOrder        A file contains a comma-separated string of group name
                        orders. The group name should match group info list in
                        the pathway score calculation step. This is useful for
                        the heatmap visualization.

optional arguments:
  -h, --help            show this help message and exit
  -o OUT_DIR, --out-dir OUT_DIR
                        Output folder name of the analysis.
  --GO                  Perform GO analysis.
  --GO-only             Only perform GO analysis. Needs to provide background
                        gene list for p-value calculation.
  -b GO_BACKGROUND_GENE_LIST, --GO-background-gene-list GO_BACKGROUND_GENE_LIST
                        Provides background gene list for GO analysis bias
                        correction. This background list should contain genes
                        involved in the splicing analysis. Required under GO-
                        only mode.
  --GOdb-versions GODB_VERSIONS
                        Specify EnrichR GO db versions. Default is the 2017
                        version used in our PNAS paper PMID: 32086391

etc.

[user@cn0861 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226