GWASPA: This function performs genome-wide association study pathway...
In carltonyfakhry/geneticsCRE: geneticsCRE is an R package that performs genome-wide association study pathway analysis (GWASPA) to identify statistically significant associations between variants on gene regulatory pathways and a given phenotype

Description Usage Arguments Value Author(s) References

This function performs genome-wide association study pathway analysis (GWASPA) to identify statistically significant associations between variants on gene regulatory pathways and a given phenotype.

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GWASPA(dataset, nCases, nControls, Signed.GWASPA = FALSE, Decorated.Pvalues = TRUE,
       threshold = 0.05, K = 10, pathLength = 5, n_permutations = 100,
       strataF = NA, nthreads = NA)

`dataset`	Filename of the phenotype data. First column must correspond to the gene symbols, and all other columns correspond to the patients. The First column must be named `Gene.Symbols` and must contain strings corresponding to the symbols of the genes. All other columns either contain a 1 if the patient has a variant in the gene, and 0 otherwise.
`nCases`	The number of cases (Must be greater than 1).
`nControls`	The number of controls (Must be greater than 1).
`Signed.GWASPA`	A boolean parameter indicating whether to compute signed-GWASPA. The default value is `Signed.GWASPA = FALSE`.
`Decorated.Pvalues`	A boolean parameter indicating whether to compute the decorated P-values. The default value is `Decorated.Pvalues = TRUE`.
`threshold`	All variants which occur in less than `threshold * 100` number of patients are kept for processing. The default value is `threshold = 0.05`.
`K`	The top `K` paths to be returned of each path length. The default value is `K = 10`.
`pathLength`	The maximum path length for which the top `K` paths will be computed. The default value is `pathLength = 5`. Note that `pathLength` cannot be set to less than 1 or greater than 5.
`n_permutations`	The number of permutations to be used for computing the p-values. The default value is 100 (The minimum acceptable value is 1).
`strataF`	Filename for the strata file. `strataF` must be a file of two columns: The first column must be named `subjid` and contains the patient names and must match the patients names in `dataset` file, and the second column named `stratum` must contain the integer corresponding to the stratum.
`nthreads`	The number of threads to be used in the parallel region of the code. Default value is `nthreads = NA`, in which case only one thread will be used.

This function returns a list with the following items:

GWASPA.Results

The top K paths for each length sorted in increasing order of the p-values. The results are stored in a data frame with the following columns:
- SignedPaths The top K signed paths for each length.
- Paths The top K paths for each length.
- Lengths The length of each path.
- Scores The score of each path.
- Pvalues The p-value of each path.
- Cases The number of cases with variants for each path.
- Controls The number of controls with variants for each path.

Decorated.Pvalues.Results

If Decorated.Pvalues = TRUE then the decorated p-values of the partitioned paths are computed. The results are stored in a data frame with the following columns:
- SignedPaths The top K signed paths for each length.
- Paths The top K paths for each length.
- Subpaths1 The first subpath partition.
- Subpaths1.Cases The number of cases with variants for Subpaths1.
- Subpaths1.Controls The number of controls with variants for Subpaths1.
- Subpaths2 The second subpath partition.
- Subpaths2.Cases The number of cases with variants for Subpaths2.
- Subpaths2.Controls The number of controls with variants for Subpaths2.
- Direction Direction of splitting along the path.
- Lengths The length of each path.
- Scores The score of each path.
- Pvalues The p-value of each path.
- DecoratedPvalues The decorated p-value of each path.
- Cases The number of cases with variants for each path.
- Controls The number of controls with variants for each path.

Carl Tony Fakhry

Franceschini, A (2013). STRING v9.1: protein-protein interaction networks, with increased coverage and integration. In:'Nucleic Acids Res. 2013 Jan;41(Database issue):D808-15. doi: 10.1093/nar/gks1094. Epub 2012 Nov 29'.

carltonyfakhry/geneticsCRE documentation built on May 13, 2019, 12:49 p.m.