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TODO
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Oct 6, 2023
See ~/Downloads/RUSH.RDATA
Since genes are dropped by voomWithDreamWeights(), the out$weights and weightsMatrix are no longer the same size:
https://github.com/GabrielHoffman/variancePartition/blob/3b7b52f14ffe47a28425e05da001fbd785874318/R/voomWithDreamWeights.R#L245C36-L245C47
Need to match names instead
Upload to Bioconductor once remaCor 0.0.16 is accepted to CRAN
June 15, 2023
Parallelize mvTest() with iterator
June 2, 2023
DONE: Reproducable RNG
# Use on.exit({})
# withRandom <- function(expr, seed = 1) {
# old <- .Random.seed
# on.exit({.Random.seed <<- old})
# set.seed(seed)
# expr
# }
# use with options() and omp_set_threads
# Use seed with LS.empirical
March 14, 2023
in deviation() add pearson residuals
need to pass in y= vobj
Feb 28
DONE: Zenith on mvTest results
April 19, 2021
Add treat and topTreat
March 30, 2021
check dream + eBayes with trend and robust
#Authors@R: c(person("Gabriel", "Hoffman", role = c("aut", "cre"), email = "gabriel.hoffman@mssm.edu"))
DONE!
March 18, 2021
info must be casted to a data.frame since DataFrame is not handled correctly
and gives error:
Error in if (inherits(possibleError, "error") && grep("the fixed-effects model matrix is column rank deficient", :
missing value where TRUE/FALSE needed
droplevels in dream
# November 2, 2020
- integrate voomWithQualityWeights() with voomWithDreamWeights
o Need to convert lm.fit() calls to dream()
o Need to dream() to return hatvalues
recommend placing a check to verify if the names in the info matrix, match with the names used in the formula and return an error if not
library(BiocParallel)
# globally specify that all multithreading using bpiterate from BiocParallel
# should use 8 cores
register(SnowParam(8))
# By default it is set to the max number of CPUs
# If you have a very long interactive session, this can crash and you get the error you see
Alternatively, you can specify and restart the parallel backend every function call
fitExtractVarPartModel(..., BPPARAM=SnowParam(8))
fitVarPartModel(..., BPPARAM=SnowParam(8))
dream(..., BPPARAM=SnowParam(8))
# July 18, 2018
Check if there is variation in each gene.
else throw error
# June 16, 2016
Improve warnings in fitVarPart and fitExtractVarPart to show which gene give a warning
# April 16, 2016
Make correlation matrix and linear mixed model equantions in vignette
the same as in supplement. The vignette examples are wrong
Add canCorPairs to the vignette
# Feb 18, 2015
add e_{i,k} in ICC correlation equation
# December 14, 2015
# Add strong warning to fitVarPartModel() that estimates memory usage. In vignette, users should be discoraged from using this interface.
# use refit() to fit the model for each gene:
# cannot do this because refit() doesn't accept new weights
# DE test: show increased power when correlation is overestimated, and decrease false positive rate when correlation is underestimated. (order is correct?)
# adjust doesn't work with varying coefficient model, but it throwings an error now
# run simulations with varying coefficient model