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PAST - Pathway Analysis Studies Tool

Installation of PAST 2.0.0-rc.

The release candidate for PAST 2.0.0 is installed or built from source using the Rust toolchain. Instructions for installing Rust can be found at https://rustup.rs/.

with cargo install

cargo install --git https://github.com/IGBB/past

from local directory

The following code installs PAST to ~/.cargo/bin/past.

git clone https://github.com/IGBB/PAST.git
cargo install --path .

The following code only builds PAST. The executable will located at target/release/past.

git clone https://github.com/IGBB/PAST.git
cargo build --release

Usage

PAST requires input data from three different files:

  • annotations in GFF format
    • these annotations must match the reference genome used for SNP discovery
    • the gene names in the annotations must match the gene names in the pathways file
  • GWAS data with the following columns
    • marker
    • sequence name
    • position
    • p-value
    • effect
  • linkage disequilibrium data with the following columns
    • first sequence name
    • first position
    • second sequence name (optional)
    • second position
    • R2
Pathways Analysis Study Tool

Usage: past [OPTIONS] --annotations <FILE> --gwas <FILE> --linkage-disequilibrium <FILE> --r-squared-cutoff <R_SQUARED_CUTOFF> --pathways <FILE> --mode <MODE> --permutations <PERMUTATIONS>

Options:
  -a, --annotations <FILE>
          a file containing annotations formatted as GFF3
  -x, --attribute <ATTRIBUTE>
          the attribute that contains gene names that match those in the
          pathways file [default: ID]
  -g, --gwas <FILE>
          a file containing GWAS data
  -c, --gwas-columns <1,2,3,4,5>
          a comma-separated value providing column numbers of required GWAS
          data; column order is marker, sequence name, position, p-value, effect
  -l, --linkage-disequilibrium <FILE>
          a file containing linkage disequilibrium data
  -k, --linkage-columns <1,2,3,4,5>
          a comma-separated value providing column numbers of required linkage
          disequilibrium data; column order is first sequence name, first
          position, second sequence name, second position, R^2
  -r, --r-squared-cutoff <R_SQUARED_CUTOFF>
          the value of R^2 at which two SNPs are considered linked [0.0 - 1.0]
  -d, --drop-different-loci
          drop linkages between positions with different loci
  -p, --pathways <FILE>
          a file containing pathways data
  -m, --mode <MODE>
          analysis mode [possible values: increasing, decreasing, both]
  -n, --permutations <PERMUTATIONS>
          the number of permutations to determine pathway significance
  -f, --membership-filter <MEMBERSHIP_FILTER>
          keep only pathways with this fraction of the genes or higher linked to
          SNPs in the GWAS data [0.0 - 1.0]
  -o, --output <DIRECTORY>
          the directory to which results will be written (will be created if it
          does not exist) [default: ./]
  -h, --help
          Print help (see more with '--help')
  -V, --version
          Print version