AfromMarkers {CAMTHC} | R Documentation

## Proportion matrix estimation from marker genes

### Description

This function estimates proportion matrix (A matrix) from observed mixture expression data based on marker genes.

### Usage

    AfromMarkers(data, MGlist, scaleRecover = TRUE)

### Arguments

`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.
`MGlist` | A list of vectors, each of which contains known markers and/or CAM-detected markers for one subpopulation.
`scaleRecover` | If TRUE, scale ambiguity of each column vector in A matrix is removed based on sum-to-one constraint on each row.

### Details

With the expression levels of subpopulation-specific marker genes, the relative proportions of constituent subpopulations are estimated by spatial median using `l1median`. Marker genes could be from unsupervised/supervised detection or from literatures. Scale ambiguity is optionally removed based on sum-to-one constraint of rows.

### Value

Return the estimated proportion matrix (A matrix).

### Examples

    #obtain data and marker genes
    data(ratMix3)
    S <- ratMix3$S
    pMGstat <- MGstatistic(S, c("Liver","Brain","Lung"))
    pMGlist.FC <- lapply(c("Liver","Brain","Lung"), function(x)
        rownames(pMGstat)[pMGstat$idx == x & pMGstat$OVE.FC > 10])

    #estimate A matrix from markers
    Aest <- AfromMarkers(ratMix3$X, pMGlist.FC)

[Package CAMTHC version 1.2.0 Index]