fcp - Function Composition

A function composition operator to chain a series of calls into a single function, mimicking the math notion of (f o g o h)(x) = h(g(f(x))). Inspired by 'pipeOp' ('|>') since R4.1 and 'magrittr pipe' ('%>%'), the operator build a pipe without putting data through, which is best for anonymous function accepted by utilities such as apply() and lapply().

Last updated 1 years ago

2.00 score 3 scripts 285 downloads

plinkFile - 'PLINK' (and 'GCTA') File Helpers

reads/write binary genotype file compatable with 'PLINK' <https://www.cog-genomics.org/plink/1.9/input#bed> into/from a R matrix; traverse genotype data one windows of variants at a time, like apply() or a for loop; reads/writes genotype relatedness/kinship matrices created by 'PLINK' <https://www.cog-genomics.org/plink/1.9/distance#make_rel> or 'GCTA' <https://cnsgenomics.com/software/gcta/#MakingaGRM> into/from a R square matrix. It is best used for bringing data produced by 'PLINK' and 'GCTA' into R workflow.

Last updated 3 years ago

2.00 score 2 scripts 251 downloads

dotgen - Gene-Set Analysis via Decorrelation by Orthogonal Transformation

Decorrelates a set of summary statistics (i.e., Z-scores or P-values per SNP) via Decorrelation by Orthogonal Transformation (DOT) approach and performs gene-set analyses by combining transformed statistic values; operations are performed with algorithms that rely only on the association summary results and the linkage disequilibrium (LD). For more details on DOT and its power, see Olga (2020) <doi:10.1371/journal.pcbi.1007819>.

Last updated 4 years ago

2.00 score 1 scripts 573 downloads