reselectMG {CAMTHC} | R Documentation

## Reselect markers by thresholding

### Description

This function generates a new list of markers based on initially detected markers by CAM and/or prior markers.

### Usage

    reselectMG(data, MGlist, fc.thres = "q0.5", err.thres = NULL)

### 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 CAM-detected markers and/or prior markers for one subpopulation.
`fc.thres` | The lower threshold of fold change to select markers, an absolute value (e.g. 10) or a quantile value after 'q' (e.g. 'q0.5', the median of fold changes of one subpopulation's input markers). Each subpopulation can have its own threshold if a vector is provided. The default is 'q0.5'. If NULL, still use the input markers.
`err.thres` | The upper threshold of reconstruction error to select markers, an absolute value or a quantile value after 'q' (e.g. 'q0.5', the median of reconstruction errors of one subpopulation's input markers; 'q1.2', the maximum error times 1.2 ). Each subpopulation can have its own threshold if a vector is provided. The default is NULL, which means no such a threshold is applied.

### Details

Considering some meaningful markers may be mistakenly filtered by preprocessing and thus missed by `CAM`, this function use the input marker gene list to estimate proportions by `AfromMarkers` and then estimate expression levels. Next, a new list of markers are generated by fold change threshold and reconstruction error threshold.

The input marker genes could also be from other supervised detection and/or from literatures. This function reselects a list of marker genes based on the input.

### Value

A list of vectors, each of which contains new selected markers for one subpopulation.

### Examples

    #obtain data and run CAM
    data(ratMix3)
    data <- ratMix3$X
    rCAM <- CAM(data, K = 3, dim.rdc= 3, thres.low = 0.30, thres.high = 0.95)
    #obtain marker genes detected by CAM with a fixed K
    MGlist <- MGsforA(rCAM, K = 3)
    #Reselect markers from all genes
    MGlist.re <- reselectMG(data, MGlist, fc.thres='q0.5')
    MGlist.re <- reselectMG(data, MGlist, fc.thres='q0.5', err.thres='q0.95')

[Package CAMTHC version 1.2.0 Index]