selectNegentropyGenes {monocle} | R Documentation

## Filter genes with extremely high or low negentropy

### Description

Examines all the genes in the CellDataSet passed in and removes all the genes that contain extremely high or low negentropies. You can specify which genes to filter out based on the boundaries you can set for expression levels and the boundaries you set for which centile to include. the function "dispersionTable" is a better form of this function.

### Usage

    selectNegentropyGenes(cds, lower_negentropy_bound = "0%",
      upper_negentropy_bound = "99%", expression_lower_thresh = 0.1,
      expression_upper_thresh = Inf)

### Arguments

`cds` | a CellDataSet object upon which to perform this operation
`lower_negentropy_bound` | the centile below which to exclude to genes
`upper_negentropy_bound` | the centile above which to exclude to genes
`expression_lower_thresh` | the expression level below which to exclude genes used to determine negentropy
`expression_upper_thresh` | the expression level above which to exclude genes used to determine negentropy

### Value

a vector of gene names

### Examples

    ## Not run:
    reasonableNegentropy <- selectNegentropyGenes(HSMM, "07%", "95%", 1, 100)

    ## End(Not run)

[Package monocle version 2.6.4 Index]