Man pages for kindlychung/CollapsABEL
An R package for quantitative CDH analysis
| appendEnv | Merge two enviroments |
| appendFromPlinkOut | Read a PLINK assoc file into a QCDH info hub |
| bedcollinfo | Collect info on shifted bed files |
| bedcollr | Shift bed files |
| catmat | Print out a matrix, in a clean format |
| checkBinaryTrait | Check whether a trait is binary |
| cleanByChrPvalsBonfer | Extract relevant SNP out of the QCDH data hub |
| cleanSnpNames | Clean up SNP names for building linear models in R |
| collapse | Genotype collapsing functions |
| contrastPlot | Contrast QCDH p values with single-SNP p values |
| dbgtrigger | Getting or setting a local boolean variable for debugging... |
| getNshiftStr | Extract shift number (as a string) from a shifted bed... |
| getPlinkParam | Get a list of parameters for passing to plinkr |
| getstem | Get the stem of a bed filename. |
| gwas | A pure R implementation of GWAS |
| plinkcollr | Apply plinkr to multiple files |
| plinkr | A wrapper for plink |
| qcdhRoutine | QCDH routine 2 |
| readcoll | Read PLINK assoc files int matrices and store them in the... |
| rep_dat | Batch version of the 'rep_models' function: |
| rep_models | Given a pair of SNPs, fit a model using single and collapsed... |
| routine1 | QCDH routine 1 |
| shiftDataByCol | Shift columns of a matrix |
| snpPairLookin.quant | Look into a pairs of SNPs |
| taskAnalyze | Analyze shifted bed files |
| taskBedsPlinkOut | Prepare shifted bed files for current task. |
| taskinfo | Prepare paths and filenames for the task |
| updateMinPvals | Calculate minial p values for QCDH |
