Run DURIAN on input data
Usage
run_durian(
path = NULL,
scrabble_parameters = c(1, 1e-06, 1e-04),
nIter_outer = 20,
nIter_inner = 20,
nSDCIters = 10000,
emDiag = FALSE,
nEM = 10,
error_out_threshold = 1e-07,
error_inner_threshold = 1e-05,
C_fn = NULL,
T_fn = NULL,
pDataC_fn = NULL,
scdata = NULL,
bulkdata = NULL,
metadata = NULL,
seur = NULL,
deconv_method = "dsLDA",
MCNITER = 5000,
MCNPARTITIONS = 5,
MCNCHAINS = 2,
MCBLOCKSIZE = 5,
MCPLOT = TRUE,
LDAPHILATENT = 2,
LDABETAPSEUDO = 0,
LDABETAEPS = 0,
LDAALPHA = 0.1,
LDANSCTHRESH = 3,
SCRNSCTHRESH = 3,
DECONVGENETHRESH = 0.01,
SCRGENETHRESH = 0.3,
MINCELLSTOPICCORP = 5,
SCRSCALESC = "ident",
SCRSCALEFACSC = 10000,
LDASCALESC = "ident",
LDASCALEBLK = "ident",
LDASCALEFACSC = 1,
LDASCALEFACBLK = 10000,
LDAINITFLAVOR = "unif",
LDARUNQC = FALSE,
LDAVERBOSE = FALSE,
MCTHINNING = 5,
MCRMCHAINS = TRUE,
MCBURNRATE = 0.25,
deconvbenchmark = NULL,
imputebenchmark = NULL,
protectedgenes = c("dummygene"),
maxT = 0,
initscrabble = FALSE,
allScr = TRUE,
limrhat = 10,
durianEps = 1e-06,
saveDeconvolutionLog = FALSE,
saveImputedStep = FALSE,
saveImputationLog = TRUE,
outerStats = FALSE,
useIrlba = TRUE,
runstability = FALSE
)