PC1VecFun {MCbiclust} | R Documentation

## 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]]))

[Package MCbiclust version 1.4.0 Index]