comp.ss.bim | Compare summary statistics and PLINK .bim data.frames |
countlines | Count number of lines in a text file |
elnet | Performs elnet |
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... |
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 |
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... |
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... |
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