| comp.ss.bim | Compare summary statistics and PLINK .bim data.frames |
| countlines | Count number of lines in a text file |
| elnet | Performs lasso |
| elnetR | Elastic net using summary statistics |
| genotypeMatrix | imports genotypeMatrix |
| group.blocks | Group blocks into chunks so as not to exhaust memory or hit... |
| indeplasso | Independent LASSO using summary statistics (a.k.a.... |
| lassosum | Function to obtain LASSO estimates of a regression problem... |
| lassosum.pipeline | Run lassosum with standard pipeline |
| lassosumR | Function to obtain LASSO estimates of a regression problem... |
| logical.vector | Function to create a logical vector based on position and... |
| matchpos | Function to match a set of variants to a reference by... |
| mcp | sj0715 Performs mcp |
| mcpR | Mcp using summary statistics |
| mcpsum | Function to obtain MCP estimates of a regression problem... |
| mcpsum.pipeline | Run mcpsum with standard pipeline |
| mcpsumR | Function to obtain MCP estimates of a regression problem... |
| merge.lassosum | Merge lassosum results |
| merge.lassosum.pipeline | Merge a list of lassosum.pipeline objects |
| multiBed3 | Multiply genotypeMatrix by a matrix |
| multiBed3sp | Multiply genotypeMatrix by a matrix (sparse) |
| ncol.bfile | Obtains the number of column (SNPs) in a PLINK bfile |
| normalize | normalize genotype matrix |
| not.a.file | A function to protect a single SNP id from being interpreted... |
| nrow.bfile | Obtains the number of individuals in a PLINK bfile |
| p2cor | Function to convert p-values to correlation via the... |
| parseargs | Function to parse arguments from command line |
| parseselect | Parse the keep/remove/extract/exclude/chr options |
| pgs | Computes polygenic scores as a genotype matrix multiplied by... |
| pgs.vec | pgs for a list of bfiles |
| plot.validate.lassosum | Plot function for 'validate.lassosum' objects |
| pseudovalidate | Function to perform pseudovalidation from a lassosum.pipeline... |
| pseudovalidation | Performs 'pseudovalidation' to select the best lambda value... |
| pseudovalidationR | Performs 'pseudovalidation' to select the best lambda value... |
| readbfile | read a PLINK bfile file into a matrix |
| read.table2 | Function to read a text file |
| ridge | Performs ridge |
| ridgeR | Ridge using summary statistics |
| ridgesum | Function to obtain RIDGE estimates of a regression problem... |
| ridgesum.pipeline | Run ridgesum with standard pipeline |
| ridgesumR | Function to obtain RIDGE estimates of a regression problem... |
| runElnet | Runs lasso with various parameters |
| runMcp | sj0717 Runs mcp with various parameters |
| runRidge | Runs ridge with various parameters |
| runScad | sj0717 Runs scad with various parameters |
| scad | sj0715 Performs scad |
| scadR | Scad using summary statistics |
| scadsum | scadsum: A package for carrying out nonconvex penalty... |
| scadsum.pipeline | Run scadsum with standard pipeline |
| scadsumR | Function to obtain SCAD estimates of a regression problem... |
| sd.bfile | Obtain the SNP-wise standard deviations from the PLINK bfile |
| selectregion | Internal function to parse extract |
| splitgenome | Function to split a set of SNPs by their position using a... |
| splitvalidate | Function to perform split-validation using output from... |
| splitvec.from.bfile | Function to create split vectors from the info in vectors of... |
| subset.lassosum.pipeline | Subset a lassosum.pipeline object by lambda and s |
| validate | Function to validate output from lassosum.pipeline with... |
