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 |
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