batchqc_pc_explained_variation {BatchQC} | R Documentation |
Returns explained variation for each principal components
batchqc_pc_explained_variation(pcs, vars, condition, batch)
pcs |
Principal components in the given data |
vars |
Variance of the Principal components in the given data |
condition |
Condition covariate of interest |
batch |
Batch covariate |
Explained variation table for each principal components
nbatch <- 3 ncond <- 2 npercond <- 10 data.matrix <- rnaseq_sim(ngenes=50, nbatch=nbatch, ncond=ncond, npercond= npercond, basemean=10000, ggstep=50, bbstep=2000, ccstep=800, basedisp=100, bdispstep=-10, swvar=1000, seed=1234) batch <- rep(1:nbatch, each=ncond*npercond) condition <- rep(rep(1:ncond, each=npercond), nbatch) pdata <- data.frame(batch, condition) modmatrix = model.matrix(~as.factor(condition), data=pdata) pca <- batchqc_pca(data.matrix, batch, mod=modmatrix) pcs <- t(data.frame(pca$x)) batchqc_pc_explained_variation(pcs, pca$sdev^2, condition, batch)