Man pages for yingxi-kaylee/ssCTPR
Cross-Trait Penalized Regression using Summary Statistics
| comp.ss.bim | Compare summary statistics and PLINK .bim data.frames |
| countlines | Count number of lines in a text file |
| elnet | Performs elnet |
| genotypeMatrix | imports genotypeMatrix |
| group.blocks | Group blocks into chunks so as not to exhaust memory or hit... |
| indepssCTPR | Independent ssCTPR based on summary statistics (a.k.a.... |
| logical.vector | Function to create a logical vector based on position and... |
| matchpos | Function to match a set of variants to a reference by... |
| merge.ssCTPR | Merge ssCTPR results |
| merge.ssCTPR.pipeline | Merge a list of ssCTPR.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 | This is to enable S3 parsing by the second argument |
| pgs.vec | pgs for a list of bfiles |
| readbfile | read a PLINK bfile file into a matrix |
| read.table2 | Function to read a text file |
| repelnet | performs elnet by blocks |
| runElnet | Runs elnet with various parameters |
| 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... |
| splitvec.from.bfile | Function to create split vectors from the info in vectors of... |
| ssCTPR | ssCTPR |
| ssCTPR.pipeline | Run ssCTPR with standard pipeline |
| subset.ssCTPR.pipeline | Subset a ssCTPR.pipeline object by lambda, s and lambda_ct |
| validate | Function to validate output from ssCTPR.pipeline with... |
