CAMASest {CAMTHC} | R Documentation

## A and S matrix estimation by CAM

### Description

This function estimates A and S matrix based on marker gene clusters detected by CAM.

### Usage

    CAMASest(MGResult, PrepResult, data, corner.strategy = 2,
      generalNMF = FALSE)

### Arguments

`MGResult` | An object of class "`CAMMGObj`" obtained from `CAMMGCluster` function.
`PrepResult` | An object of class "`CAMPrepObj`" obtained from `CAMPrep` function.
`data` | Matrix of mixture expression profiles which need to be the same as the input of `CAMPrep`. Data frame, SummarizedExperiment or ExpressionSet object 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.
`corner.strategy` | The method to detect corner clusters. 1: minimum sum of margin-of-errors; 2: minimum sum of reconstruction errors. The default is 2.
`generalNMF` | If TRUE, the decomposed proportion matrix has no sum-to-one constraint for each row. Without this constraint, the scale ambiguity of each column vector in proportion matrix will not be removed. The default is FALSE.

### Details

This function is used internally by `CAM` function to estimate proportion matrix (A), subpopulation-specific expression matrix (S) and mdl values. It can also be used when you want to perform CAM step by step.

The mdl values are calculated in three approaches: (1) based on data and A matrix in dimension-reduced space; (2) based on original data with A matrix estimated by transforming dimension-reduced A matrix back to original space; (3) based on original data with A directly estimated in original space. A and S matrix in original space estimated from the latter two approaches are returned. mdl is the sum of two terms: code length of data under the model and code length of model. Both mdl value and the first term (code length of data) will be returned.

### Value

An object of class "`CAMASObj`" containing the following components:

`Aest` | Estimated proportion matrix from Approach 2.
`Sest` | Estimated subpopulation-specific expression matrix from Approach 2.
`Aest.proj` | Estimated proportion matrix from Approach 2, before removing scale ambiguity.
`Ascale` | The estimated scales to remove scale ambiguity of each column vector in Aest. Sum-to-one constraint on each row of Aest is used for scale estimation.
`AestO` | Estimated proportion matrix from Approach 3.
`SestO` | Estimated subpopulation-specific expression matrix from Approach 3.
`AestO.proj` | Estimated proportion matrix from Approach 3, before removing scale ambiguity.
`AscaleO` | The estimated scales to remove scale ambiguity of each column vector in AestO. Sum-to-one constraint on each row of AestO is used for scale estimation.
`datalength` | Three values for code length of data. The first is calculated based on dimension-reduced data. The second and third are based on the original data.
`mdl` | Three mdl values. The first is calculated based on dimension-reduced data. The second and third are based on the original data.

### Examples

    #obtain data
    data(ratMix3)
    data <- ratMix3$X

    #preprocess data
    rPrep <- CAMPrep(data, dim.rdc = 3, thres.low = 0.30, thres.high = 0.95)

    #Marker gene cluster detection with a fixed K
    rMGC <- CAMMGCluster(3, rPrep)

    #A and S matrix estimation
    rASest <- CAMASest(rMGC, rPrep, data)

[Package CAMTHC version 1.4.0 Index]