selectNegentropyGenes: Filter genes with extremely high or low negentropy

Description Usage Arguments Value Examples

View source: R/utils.R

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

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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

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

## End(Not run)

monocle documentation built on April 6, 2018, 2:02 a.m.