patternMarkers {CoGAPS} | R Documentation

## compute pattern markers statistic

### Description

calculate the most associated pattern for each gene

### Usage

    patternMarkers(object, threshold = "all", lp = NA, axis = 1)

    ## S4 method for signature 'CogapsResult'
    patternMarkers(object, threshold = "all",
      lp = NA, axis = 1)

### Arguments

`object` | an object of type CogapsResult
`threshold` | the type of threshold to be used. The default "all" will distribute genes into pattern with the lowest ranking. The "cut" thresholds by the first gene to have a lower ranking, i.e. better fit to, a pattern.
`lp` | a vector of weights for each pattern to be used for finding markers. If NA markers for each pattern of the A matrix will be used.
`axis` | either 1 or 2, specifying if pattern markers should be calculated using the rows of the data (1) or the columns of the data (2)

### Value

By default a non-overlapping list of genes associated with each `lp`.

### Examples

    data(GIST)
    pm <- patternMarkers(GIST.result)

[Package CoGAPS version 3.6.0 Index]