doBISEPAnalysis: BISEP Analysis
In chapmandu2/CollateralVulnerability2016: Collateral Vulnerability Pipeline

Description Usage Arguments Value

The BISEP analysis function identifies genes with bimodel expression profiles. See BiSEp documentation. Note that the version of BISEP used is slightly modified and not that from the BiSEp package - see BISEP_cv for more details.

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doBISEPAnalysis(con, genes_n = 1e+05, table_name = "tcga_rnaseq_data",
  log2_transform = TRUE, gene_var_th = 0.2, gene_naprop_th = 0.3,
  seed_val = NULL)

`con`	A `SQLiteConnection` object
`genes_n`	Permits a random subsample of genes to be analysed rather than the full set. Default 100000 - ie all.
`table_name`	The table in the SQLite database containing the data. The table should have fields named patient_id, gene_id and value where gene_id is an ensembl id. Default tcga_rnaseq_data
`log2_transform`	Boolean operator to determine whether data should be log2 transformed. Default `TRUE`
`gene_var_th`	Genes with very low variance can cause BISEP to fail. Increasing the gene variance threshold parameter can filter out these genes. Default 0.2
`gene_naprop_th`	Genes with a higih proportion of NA values can cause BISEP to fail. Decreasing the proportion of NA's filter can filter out these genes. Default 0.3.
`seed_val`	Setting this parameter ensures that consistent BISEP p-values are returned from run to run but there is no parallelisation so the analysis will take longer. See `set.seed` for more details. Default is NULL - no seed set.