MGstatistic {CAMTHC} | R Documentation |
This function computes One-Versus-Everyone Fold Change (OVE-FC) from subpopulation-specific expression profiles. Bootstrapping is optional.
MGstatistic(data, A = NULL, boot.alpha = NULL, nboot = 1000, cores = NULL)
data |
A data set that will be internally coerced into a matrix. Each row is a gene and each column is a sample. Data should be in non-log linear space with non-negative numerical values (i.e. >= 0). Missing values are not supported. All-zero rows will be removed internally. |
A |
When data are mixture expression profiles, A is estimated proportion matrix or prior proportion matrix. When data are pure expression profiles, A is a phenotype vector to indicate which subpopulation each sample belongs to. |
boot.alpha |
Alpha for bootstrapped OVE-FC confidence interval. The default is 0.05. |
nboot |
The number of boots. |
cores |
The number of system cores for parallel computing. If not provided, the default back-end is used. |
This function calculates OVE-FC and bootstrapped OVE-FC which can be used to identify markers from all genes.
A data frame containing the following components:
idx |
Numbers or phenotypes indicating which subpopulation each gene could be a marker for. If A is a proportion matrix without column name, numbers are returned. Otherwise, phenotypes. |
OVE.FC |
One-versus-Everyone fold change (OVE-FC) |
OVE.FC.alpha |
lower confidence bound of bootstrapped OVE-FC at alpha level. |
#data are mixture expression profiles, A is proportion matrix data(ratMix3) MGstat <- MGstatistic(ratMix3$X, ratMix3$A) ## Not run: MGstat <- MGstatistic(ratMix3$X, ratMix3$A, boot.alpha = 0.05) #enable boot ## End(Not run) #data are pure expression profiles without replicates MGstat <- MGstatistic(ratMix3$S) #boot is not applicable ## Not run: #data are pure expression profiles with phenotypes S <- matrix(rgamma(3000,0.1,0.1), 1000, 3) S <- S[, c(1,1,1,2,2,2,3,3,3,3)] + rnorm(1000*10, 0, 0.5) MGstat <- MGstatistic(S, c(1,1,1,2,2,2,3,3,3,3), boot.alpha = 0.05) ## End(Not run)