rmRNAseq (version 0.1.0)

TC_CAR1_sc: A Wrap Function to analyze a Simulated Data - All Cases

Description

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.

Usage

TC_CAR1_sc(RFIanalysis, scenario, EE, DE, C.matrix, Subject, Time, Nboot,
  nrep, ncores, name_dir_sim = NULL, print.progress = FALSE,
  saveboot = FALSE)

Arguments

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 ncores is 1.

name_dir_sim

name of directory to contain the output and result of this function

print.progress

TRUE or FALSE, printing the process or not.

saveboot

TRUE or FALSE to save or not save bootstrap output

Value

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.

Examples

# NOT RUN {
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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