Description Usage Arguments Value Examples
This function does the following: 1. Generating a simulated
counts data set consisting of EE genes, and DE genes with
respect to some contrast from a ideal case, i.e., the counts
are generated from corCAR1 structure, or misspecified case, i.e., the counts
are generated from corSymm structure; analyzing this simulated data set
using methods: TC_CAR1
,
voomlimmaFit
, edgeRFit
, DESeq2Fit
.
1 2 3 | TC_CAR1_sc(RFIanalysis, scenario, EE, DE, C.matrix, Subject, Time, Nboot,
nrep, ncores, name_dir_sim = NULL, print.progress = FALSE,
saveboot = FALSE)
|
RFIanalysis |
the output from RFI RNA-seq dataset. In the ideal simulation case, it is res from TC_CAR1, in the misspecified case, it is res from TC_Symm |
scenario |
either 2- 'Symm' or 1- 'CAR1' |
EE |
number of EE genes |
DE |
number of DE genes |
C.matrix |
is a list of matrix Ci in testing H0: Ci*beta = 0. |
Subject |
a vector of subjects or experimental units. |
Time |
a vector of time points. |
Nboot |
number of bootstrap replicates, default is 100. |
nrep |
index of sim replicate |
ncores |
number of cores for embarrassingly parallel procedure. Default
value of |
name_dir_sim |
name of directory to contain the output and result of this function |
print.progress |
|
saveboot |
|
R, V, FDR, PAUC, and AUC of all 7 methods (2 oracles with unshrunken and shrunken) with FPR = 0.05, 0.10, 0.20 for each S, R, V, FDR, PAUC.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | data(res)
data(resSymm)
data(design)
data(covset)
RFIanalysis <- list(CAR1 = res, Symm = resSymm)
C.matrix <- list()
# test for Line main effect
C.matrix[[1]] <- limma::makeContrasts(line2, levels = design)
names(C.matrix) <- c("line2")
scenario <- 1; EE <- 3; DE <- 2; ncores <- 1; Subject <- covset$ear;
Time <- covset$time; Nboot <- 2; nrep <- 1;
name_dir_sim <- NULL
print.progress <- FALSE; saveboot <- FALSE;
TC_Symm_scOut <- rmRNAseq:::TC_CAR1_sc(RFIanalysis, scenario, EE, DE, C.matrix,
Subject, Time, Nboot, nrep, ncores, name_dir_sim , print.progress, saveboot)
names(TC_Symm_scOut)
|
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