chris1221/corge

Evaluation of Simultaneous Inference Methods for the Human Genome.

coRge: Software for the Examination of Multiple Correction Methodologies in Accurate Genomic Environments

Status:

Branch	Travis-CI	Appveyor	Coverage	CRAN	Downloads	Publication
master						GitXiv
devel						GitXiv

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To install:

if(!require(devtools)) install.packages("devtools")
devtools::install_github("Chris1221/coR-ge")

To run:

library(coRge)

coRge::analyze(gen = genEx, summary = exampleSamp, output = "/dev/null") 

If everything is configured properly, this should return 0. If it does, please move on to the quick start guide and tutorial.

corge's Issues

Adjust p values by grouping vector [correct() and analyze()]

Need to alter correct.R or analyze.new.R to account for the fact that grouping variables may be included.

Issues Remaining

January 12 Meeting

• The clusters aren't obviously separable, so maybe add as a third dimension a density peak to see if the groups really are different in the following:

• Incorporate true positive gradient instead of absolute number of TPs
• Sweep over concentrations for cluster enrichment
• UK10K Data access

Non finite elements introduced in effect size calculation

Clean up namespace conflict warnings with @ImportFrom

Logging with futile.logger and pass up threshold

Definitely need to do this, but maybe not by Monday. Might be as simple as replacing message( with flog.info( but check this first.

snps out of scope in coRge::phen

[v0.6.3.9000] Singular Matrices in c(1, gen)

Dealing with this by Moore-Penrose pseudo-inverse of matrix.

arma::pinv()

Sub Script function

• Create cluster submission script within inst/bash
• Create wrapped function for sub so don't have to leave R, ie

if(!require(pacman)) install.packages("pacman", repos = uT)
p_load(foreach, SnowMC)

install_github("Chris1221", "coRge")

uT = cran repo
foreach(i = 1:10) %:% foreach(j = 1:10) %do% sub(i,j) #from within interactive session

Unsigned to signed int comparison [-wSign-compare]

ld.cpp:38:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(uword i = 0; i < nCausal; i++){

Probably okay. This comes from the counter in RcppArmadillo.

Remedy .GlobalEnv() workaround for `samp`

Circumvent need for coRge::gen2r()

This is way too long, maybe create a vector with three entries for each es and simply multiply the matrices. This has to be faster. Have to make sure that 0*x = 0 and that the 0s don't contribute to rowsums. they shouldn't but just make sure.

[v0.6.4.9000] Deprecate i and j args in favour of path to file / dir

data.table::fread() / coR-ge::gen2r() => readlines() + foreach::dopar()

Vectorize SNPTEST2R.R

using foreach

Export group and group_name arguements

Vignette

CentOS 6 Compatibility (g++ < 4.6)

Oh boy. This is going to be a headache.

Failed attempts at speeding up reading (i.e. things which are not faster than fread).

Attempts at speeding up the reading and converting of .gen files.

This thread exists as a warning and reminder to myself of how truly awful I am at programming.

Add in gene "mode"

Mode arguement must be changed in analyze.R along with correct.R and stratify.R.

Another option would be to harmonize the entire function, but I don't think I have the time right now.

base::for => doMC::foreach [Oxford to R format conversion]

Convert gen2r.R to use better looping constructs. Additionally check to see number of threads avvailble to multicore.

Import shell scripts from inst/bash in sim.gen()