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\dontrun{} to \donttest{} in .Rd
filesDESCRIPTIONsample()Roxgyen2 & devtools::check()tests/testthat/test-BasicRFunctionality.R,
test-ResultsFollowupAnalysisAndPlotting.R,
test-Stephens2013PLoSONE.globallipids.GLCfuncs.R, and
test-Stephens2013PLoSONE.test.funcs.RModels output more user-friendly versions
Models and directed users
in main vignette to utilize GetModelPriorMatrix() for a
more interpretable version of ModelPriorsreleases on the github repo#pkgdown website for the github repoREADME.mdroxygen2 comments &
examplesGetModelPriorMatrix() in
ResultsFollowupAnalysisAndPlotting.R so that
SigmaAlphas is given a default value to begin with and
therefore positioned after LogFilebmass() with some
data already created (ie a merged dataset, a phenotype correlation
matrix, and priors)
ZScoresCorMatrix should
have the same phenotype order as DataSourcesPassChecksForDataSources.R
additionsCheckMergedDataSources as an analogue to
CheckIndividualDataSources for when a merged dataset is
provided.MergeDataGWASAnnotateAndGetMarginalSNPs.R) & that A1
part of ExpectedColumnNamesGetModelPriorMatrix() in the advanced, introductory
vignette*.R fileRoxygen2 comments and the first vignette, and
finished creating unit testsdevtools::check() results and made
required editsbmass.R,
Stephens2013PLoSONE.globallipids.GLCfuncs.R, &
Stephens2013PLoSONE.test.funcs.Rbmass.R changed GWASThreshFlag from
0/1 to FALSE/TRUE
DetermineAndApplyPriors in
GetResultsFromMarginalSNPsAndFormat.RGWASThreshFlag to default as
TRUEResultsFollowupAnalysisAndPlotting.R removed a large
number of the functions that were potentially more manuscript-specific
and likely to become deprecated (most of which were
plotting-related)library() calls to proper use of
Imports in DESCRIPTION fileGetResultsFromMarginalSNPsAndFormat.R (ie
CHECK_0 -- Prob: Throw an error/fail thing here)bmass.R changed PrintLogStatements to
PrintProgressbmass.R removed the loadings of
library(ggplot2) and library(reshape2)bmass.R removed the commented out
ExploreBestModelsUsingPosteriors()bmass.R & main bmass() call added
"A1" to ExpectedColumnNamesModels and ModelPriors outputs to more
user-friendly versions
Models and possibly
condense ModelPriors across all the SigmaAlphasbmass() with some
data already created (ie a merged dataset, a phenotype correlation
matrix, and priors)
ZScoresCorMatrix should
have the same phenotype order as DataSourcestest-ResultsFollowupAnalysisAndPlotting.R, particularly
evaluate issues with GetTopModelsPerSNPViaPosteriorstest-Stephens2013PLoSONE.globallipids.GLCfuncs.R and
test-Stephens2013PLoSONE.test.funcs.Rmerge() unit tests in
tests/testthat/test-BasicRFunctionality.RCheckMergedDataSources as an analogue to
CheckIndividualDataSources for when a merged dataset is
provided.PassChecksForDataSources.R additions
Marker column, input
MergeDataSources file, etc… as wellMergeDataGWASAnnotateAndGetMarginalSNPs.R) & that A1
part of ExpectedColumnNameswrite(...stderr()) is functioning in
bmass.R (since it seems like that might not be occuring
like I was expecting it to?)ResultsFollowupAnalysisAndPlotting.R (eg
GetModelPriorMatrix,
GetTopModelsPerSNPViaPosteriors, ``, etc…)GWASThreshFlag &
GWASThreshValue functionalityMergeDataSources() from
AnnotateMergedDataWithGWASSNPs() in main
bmass() call since the two parts take very different times,
ie former is longer than the latter.AnnotateDataWithGWASSNPs to a quicker version
where the loop is over the GWAS SNPs and not the merged dataset; taking
advantage of in-line conditional statements as well for row
selection.PrintMergedData to indicate whether
bmassOutput$MergedDataSources should be included as part of
the output and not made NULL. This would be for whether a
user wants to save a copy of MergedDataSources and reuse it
for later runs.bmass() input variable
ZScoresCorMatrix that allows users to manually use a
specified phenotype correlation matrix.DetermineAndApplyPriors to output
PreviousSNPs$logBFs in the sections when
ProvidedPriors is not NULL and when
UseFlatPriors is TRUE.Marker column as an expectation for input
files in lieu of the ChrBP column I constructed. If
ChrBP is desired to be used as marker names, it can be
created by users before submitting the files to
bmass().GWASsnps not only
by input GWASsnps file but also by a GWAS p-value threshold
(via GWASThreshFlag &
GWASThreshValue)PreviousSNPs sections in
GetResultsFromMarginalSNPsAndFormat.R (both
DetermineAndApplyPriors and
FinalizeAndFormatResults) with
...if (!is.null(GWASsnps)) {... encapsulation as
neededwrite(..., stderr()) statements to mimic calls
to LogFile1 to be produced as bmass() runs, eg
giving user a live look into how/where the script is proceeding. These
statements are a bit more broad/higher-level than the
LogFile1 calls themselves. Also created
PrintLogStatements (default FALSE) to turn
this functionality on/off.MergeDataSources, added in section post-merge that
checks SNPs still have correct MAF (eg <= .5).
CheckIndividualDataSources section.
CheckDataSourceMAFIsMAF and
CheckDataSourceMAFFixed functions.bmass.devlog.vs1.txt to
bmass.devlog.vs1.md.GetSumAcrossSigmaAlphas_withPriors.$ from atomic
vector style calling in AnnotateDataWithGWASSNPs after move
away from apply function.logBF to logBFs.ProvidedPriors in
CheckIndividualDataSources to expect 3 ^
(length(DataSources) * length(SigmaAlphas)), not 3 ^
length(DataSources).bmass.R changed
if (is.null(PrintMergedData)) { to
if (PrintMergedData == FALSE) {, and changed default value
of PrintMergedData from NULL to
FALSE.posteriorprob so that prior in
apply(prior * 10^lbf,2,normalize) now specifies the proper
matrix dimensions rather than assuming, given proper length, prior will
be multiplied along lbf filling column-wise first (which it does by
default).MergedDataSources as one of the return values of
ProcessMergedAndAnnotatedDataSources in
MergeDataGWASAnnotateAndGetMarginalSNPs.RSigmaAlphas as an input to
GetModelPriorMatrix in
ResultsFollowupAnalysisAndPlotting.RZScoreHitFlag1 cutoff by including
2*pnorm...if (nrow(SummaryOfTopModels) > 1) {... to
GetTopModelsPerSNPViaPosteriors in
ResultsFollowupAnalysisAndPlotting.R because (apparently)
reordering a single-row matrix in the way that I’m doing it messes up
its classification as a matrix; after this command, and loss of matrix
class, the following colnames() command throws an error.
This does not occur when there are more than one row and an actualy
‘re-ordering’ occurs (presumably).CheckMergedDataSources as an analogue to
CheckIndividualDataSources for when a merged dataset is
provided.PassChecksForDataSources.R additions
Marker column, input
MergeDataSources file, etc… as wellExpectedColumnNamestestthatPrepareData.R to
better designated .R filesNewHits to
NewSNPsNewSNPs creation section to after creation of
logBFs and PosteriorProbabilities matrices
from MarginalHits; moved NewHits <- NULL initialization
section of entire codeLogFile1 to LogFileProvidedPriors to be the first option in the
if/elseif/else block that also checks is.null(GWASsnps)...,
etc…testthat, including for
basic R functionality, PassChecksForDataSources.R, andGWASsnps_AnnotateWindowMarginalHits to
MarginalSNPs, including in variable names, eg
PruneMarginalHits and
PruneMarginalHits_bpWindowGetLogBFsFromData into
GetLogBFsFromData and
DetermineAndApplyPriorsGetResultsFromMarginalSNPs.R to
GetResultsFromMarginalSNPsAndFormat.R, moved
FinalizeAndFormatResults() back to
GetResultsFromMarginalSNPsAndFormat.R, and removed
FormatAndPrepareResults.RExploreBestModelsUsingPosteriors to put code
chunks dealing with posteriors and related analyses such as
BestClassFollowupResultsAnalysisFormattingAndPlotting.R to
ResultsFollowupAnalysisAndPlotting.RExploreBestModelsUsingPosteriors into
ResultsFollowupAnalysisAndPlotting.RTestData1.txt, TestData2.txt, and
TestSigSNPs.txt to bmass_TestData1.txt,
bmass_TestData2.txt, and
bmass_TestSigSNPs.txtCheckCharacterFormat to
CheckCharacterClassCheckDataSourceDirectionColumn, moving from a for loop to
use of
...if (length(...[...!= "+" & ... != "-"]) > 0 )...LogFile to bmassOutput$LogFile in
main bmass.R filebmassOutput as a way to hold temp variables since
can output and assign multiple variables via the list structure and
self-made functions. Eg cannot do
c(var1, var2) <- function(input1), but can do
list1[c("var1", "var2")] <- function(input1) assuming
function outputs a list with two entriespaste(..., collapse=" ") at end of
stop() calls that had
DataSources[!DataSources...]-type error messages
stop() seems to already have some automatic
paste()-type calls? Eg how it can incorporate my call to
paste() at the end without any additional
specificationsLogBF to logBF in all instances
except for function name GetLogBFsFromDataif (!is.null(bmassSeedValue)) {... section to
within the else{...} portion of the
if (!is.null(ProvidedPriors)) {... blockPriors_Used to
ModelPriors_UsedGetSumAcrossSigmaAlphas_withPriors changed
ModelPriors to ModelPriors_MatrixGetSumAcrossSigmaAlphas_withPriors
in FinalizeAndFormatResults, including
...matrix(...nrow=length(ModelPriors)...)... to make the
number of rows explicitbmassOutput to include the
list() structure of MaringalSNPs,
NewSNPs, and PreviousSNPsbmassOutput:
NewSNPs, NewSNPs$SNPs,
NewSNPs$logBFs, NewSNPs$Posteriors
bmassOutput variables and associated lists
at beginning of functionSNPMarginalpValThreshold to
SNPMarginalUnivariateThreshold and
SNPMarginalMultivariateThresholdPosteriorProbabilities to
PosteriorsMarginalSNPs, NewSNPs, and
PreviousSNPs setup with list() formatting
PreviousSNPs from
GWAShitsBestModel_Posterior to PreviousSNPs
mostly has a reminder/placeholder for the time being to expand on it
later for both NewSNPs and MarginalSNPsbmassOutput warranted moving to version 0.1.0
BestModel as a variable for every SNP? Include
posterior as well as the model itself?ModelMatrix,
AllBut1Assoc, and MarginalPosteriors into this
area?bmassOutput variableis.null(GWASsnps) &
else subsectionsPruneMarginalHits
flaglogBFs and PosteriorProbabilities
output matrices
GetSumAcrossSigmaAlphas_withPriors()NewSNPs output variable, in conjunction with
GWASlogBFMinThresholdbmassOutputbmassOutput:
MarginalSNPsModelPriorslogBFsPosteriorProbabilitiesGWASlogBFMinThresholdNewSNPsbmassOutputbmassOutput associated variables
bmassOutput resultsThese binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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