PLASMA (PopuLation Allele-Specific MApping) is a statistical fine-mapping method for functional data using QTL and allelic-imbalance signal.
Preprint for the PLASMA method
Developed at the Gusev Lab at the Dana Farber Cancer Institute / Harvard Medical School.
PLASMA utilizes Python 2.7 requires the following Python packages for core functionality:
The following packages are optional, but are used for pre/post-processing:
All packages can be installed using Python's pip package manager.
To download PLASMA, click "Clone or Download" or enter:
git clone https://github.com/austintwang/plasma
The run_plasma.py script conducts fine-mapping of a single locus with default PLASMA parameters and outputs.
The script requires the following files:
- Two text files (one for each haplotype), specifying the haplotype-specific genotypes, across samples and marker. Each row should represent an individual, and each column should represent a marker. The ordering of samples and markers should be the same for both files.
- Two text files (one for each haplotype), specifying the haplotype-specific phenotypes (e.g. read counts) across samples. The order of samples should be the same as that of the genotype files.
- A text file, specifying the total phenotype across samples. If none is provided, then the total phenotype is assumed to be the sum of the haplotype-specific phenotypes.
Other parameters include:
- Individual-level or global beta-binomial overdispersions.
- AS-Only and QTL-only modes, where the total phenotype and allele-specific phenotypes are ignored, respectively.
- Search parameters, including the maximum number of causal variants and the search mode (exhaustive or stochastic shotgun search)
- The confidence level when creating the credible set
The script outputs two files in the specified output directory:
cset.txt: The minimal set of markers that contains the set of true causal markers, at the specified confidence level.1and0denote that a marker is included in and excluded from the credible set, respectively. The order of the markers is the same as that in the genotype files.ppas.txt: The marginal posterior probabilities of each marker being causal.
Usage of the script is as follows:
usage: run_plasma.py [-h] [--total_exp_path TOTAL_EXP_PATH]
[--overdispersion_path OVERDISPERSION_PATH]
[--overdispersion_global OVERDISPERSION_GLOBAL]
[--as_only] [--qtl_only] [--search_mode SEARCH_MODE]
[--max_causal MAX_CAUSAL] [--confidence CONFIDENCE]
hap_A_path counts_A_path hap_B_path counts_B_path out_dir
positional arguments:
hap_A_path Path to haplotype A genotypes file
counts_A_path Path to haplotype A mapped counts file
hap_B_path Path to haplotype B genotypes file
counts_B_path Path to haplotype B mapped counts file
out_dir Path to output directory
optional arguments:
-h, --help show this help message and exit
--total_exp_path TOTAL_EXP_PATH, -t TOTAL_EXP_PATH
Path to total QTL phenotype file (Default: Sum of
counts files)
--overdispersion_path OVERDISPERSION_PATH, -o OVERDISPERSION_PATH
Path to individual-level AS overdispersion file
(Default: Global overdispersion)
--overdispersion_global OVERDISPERSION_GLOBAL, -g OVERDISPERSION_GLOBAL
Global AS overdispersion (Default: 0)
--as_only, -a AS-Only Mode
--qtl_only, -q QTL-Only Mode
--search_mode SEARCH_MODE, -s SEARCH_MODE
Causal configuration search mode (Default:
"exhaustive")
--max_causal MAX_CAUSAL, -m MAX_CAUSAL
Maximum number of causal configurations searched
(Default: 1)
--confidence CONFIDENCE, -c CONFIDENCE
Credible set confidence level (Default: 0.95)
PLASMA additionally has a Python API, which exposes the full feature set of PLASMA. Documentation for the PLASMA Python API is currently in progress.
Features of the API include:
- Alternative data input formats, including direct use of association statistics
- User specification of hyperparameters, including heritabilities and correlations between the AS and QTL phenotypes
- Additional fine-mapping outputs
- Colocalization analysis across multiple quantitative allele-specific phenotypes
- An allele-specific simulation framework for quantitative phenotypes
- Ability to extend PLASMA via subtyping
To see the latest code, check the dev branch.
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