PC1VecFun: Calculate PC1 vector of found pattern

In rbentham/MCbiclust: Massive correlating biclusters for gene expression data and associated methods

Calculate PC1 vector of found pattern

Description

The correlations found between the chosen geneset in a subset of samples can be summarised by looking at the first principal component (PC1) using principal coponent analysis (PCA).

Usage

PC1VecFun(top.gem, seed.sort, n)

Arguments

top.gem	Gene expression matrix containing only highly correlating genes
seed.sort	Ordering of samples according to strength of correlation
n	Number of samples to use in calculation of PC1

Details

PC1VecFun() takes a gene expression matrix and the sample ordering and fits a PC1 value to all the samples based on a PCA analysis done on the first n samples.

Value

PC1 value for each sample

Examples

data(CCLE_small)
data(Mitochondrial_genes)

mito.loc <- (row.names(CCLE_small) %in% Mitochondrial_genes)
CCLE.mito <- CCLE_small[mito.loc,]

set.seed(102)
CCLE.seed <- FindSeed(gem = CCLE.mito,
                      seed.size = 10,
                      iterations = 100,
                      messages = 1000)

CCLE.sort <- SampleSort(gem = CCLE.mito,seed = CCLE.seed,sort.length = 11)

# Full ordering are in Vignette_sort in sysdata.rda
CCLE.samp.sort <- MCbiclust:::Vignette_sort[[1]]

CCLE.pc1 <- PC1VecFun(top.gem = CCLE.mito,
                      seed.sort = CCLE.samp.sort,
                      n = 10)

CCLE.cor.vec <-  CVEval(gem.part = CCLE.mito,
                            gem.all = CCLE_small,
                            seed = CCLE.seed,
                            splits = 10)

CCLE.bic <- ThresholdBic(cor.vec = CCLE.cor.vec,sort.order = CCLE.samp.sort,
                         pc1 = as.numeric(CCLE.pc1))

CCLE.pc1 <- PC1Align(gem = CCLE_small, pc1 = CCLE.pc1,
                     cor.vec = CCLE.cor.vec ,
                     sort.order = CCLE.samp.sort,
                     bic =CCLE.bic)

CCLE.fork <- ForkClassifier(CCLE.pc1, samp.num = length(CCLE.bic[[2]]))

rbentham/MCbiclust documentation built on Feb. 5, 2024, 7:44 a.m.