mixing_matrix_computation: Calculate and scale the mixing matrix

In UNDO: Unsupervised Deconvolution of Tumor-Stromal Mixed Expressions

Description

Calculate the mixing matrix based on the output from marker_gene_selection(), and scale the mixing matrix to make the sum of proportions from tumor and stroma equal to 1. The pure expression levels of tumor and stroma are also computed.

Usage

mixing_matrix_computation(X, a1, a2, dimenMatrix)

Arguments

X	Gene expression data matrix
a1	The slope of marker genes in source 1
a2	The slope of marker genes in source 2
dimenMatrix	The dimention reduction matrix used to recover mixing matrix for all the samples

Value

Aest	estimated mixing matrix
Sest	estimated pure gene expression of two sources

Author(s)

Niya Wang ([e-mail])

Examples

a1<- matrix(runif(2),2,1)
a2<- matrix(runif(2),2,1)
X <- 1000*matrix(runif(20000),10000,2)
dimenMatrix <- NULL
Deconv <- mixing_matrix_computation(X, a1, a2, dimenMatrix)

Example output

Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

UNDO documentation built on Nov. 8, 2020, 7:53 p.m.