Description Usage Arguments Value Author(s) References See Also Examples
Hard-threshold estimators based on the raw estimates of the log fold change and their p-values.
1 2 3 4 5 | nhard.threshold.est(x, y = NULL, opt = c("fold.change","twer", "fwer", "lfdr",
"lfdr0", "lfdr1"), alpha = 0.05, pval.fun = t.test, arglis.pvalfun = list(),
alternative = "two.sided", ...)
nfc.threshold.est(x, y = NULL, threshold = 0.5, ...)
|
x |
Input data matrix: features(rows) x samples (columns). See examples. |
y |
Optional input data matrix. |
opt |
Option for selecting the type of estimator, it is a character:
|
alpha |
Hard threshold value for the general function |
threshold |
Hard threshold value for function |
pval.fun |
Function to compute p-values from the input data. Usually: "t.test", "wilcox.test", etc. |
alternative |
Argument for input function |
arglis.pvalfun |
Further arguments for the input function |
... |
Arguments to pass to function |
A vector of length equal to the total number of features (i.e. proteins, genes,...).
Code: Zahra Montazeri, Corey M. Yanofsky, David R. Bickel and Marta Padilla (modifications)
Documentation: Alaa Ali and Marta Padilla
Montazeri, Z., Yanofsky, C. M., & Bickel, D. R. (2010). Shrinkage estimation of effect sizes as an alternative to hypothesis testing followed by estimation in high-dimensional biology: Applications to differential gene expression. Statistical Applications in Genetics and Molecular Biology, 9, 23.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 | #simulate some data sets: matrices of log-abundance levels
nsam<-10 #number of individuals
nfeat<-40 #number of features (metabolites, genes,...)
diffs<-c(1:7) #features with differential log-abundance levels
lfc<-5 #differential quantity
# create data sets:
x <- matrix(runif(nfeat*nsam), nrow = nfeat, ncol = nsam) #case
y <- matrix(runif(nfeat*nsam), nrow = nfeat, ncol = nsam) #control
x[diffs,] <- x[diffs,] + lfc
# hard threshold estimator on fold change: ----------
z1 <- nhard.threshold.est(x=x,y=y,alpha=0.3,opt="fold.change")
z2 <- nfc.threshold.est(x=x,y=y,threshold=0.5)
# other options: -----
z4 <- nhard.threshold.est(x=x,y=y,pval.fun=t.test,opt="TWER")
z5 <- nhard.threshold.est(x=x,y=y,alpha=0.05,opt="FWER")
z6 <- nhard.threshold.est(x=x,y=y,pval.fun=wilcox.test,opt="LFDR")
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