patternMarkers {CoGAPS} | R Documentation

## patternMarkers

### Description

patternMarkers

### Usage

    patternMarkers(Amatrix = NA, scaledPmatrix = FALSE, Pmatrix = NA,
      threshold = "all", lp = NA, full = FALSE)

### Arguments

`Amatrix` | A matrix of genes by weights resulting from CoGAPS or other NMF decomposition
`scaledPmatrix` | logical indicating whether the corresponding pattern matrix was fixed to have max 1 during decomposition
`Pmatrix` | the corresponding Pmatrix (patterns X samples) for the provided Amatrix (genes x patterns). This must be supplied if scaledPmatrix is FALSE.
`threshold` | # the type of threshold to be used. The default "all" will distribute genes into pattern with the lowest ranking. The "cut" thresholding 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.
`full` | logical indicating whether to return the ranks of each gene for each pattern

### Value

By default a non-overlapping list of genes associated with each `lp`. If `full=TRUE` a data.frame of genes rankings with a column for each `lp` will also be returned.

[Package CoGAPS version 3.0.2 Index]