findHVG: Finding highly variable genes (HVG) based on Gini...

Description Usage Arguments Value

View source: R/descend.R

Description

The function finds highly variable genes based on the Gini or CV estimates from DESCEND. A quantile natural cubic spline regression of the estimated selected criteria on the log of the estimated mean for the genes is performed as the general trend. HVGs are selected as the genes whose normalized difference between its estimates and the trend is larger than a threshold. For examples, see runDescend

Usage

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findHVG(descend.list, criteria = c("Gini", "CV"), quantile = 0.7,
  threshold = 3, plot.result = T, spline.df = 5)

Arguments

descend.list

a list of descend objects computed from runDescend

criteria

the cirteria of HVG finding, either "Gini" or "CV"

quantile

quantile of the quantile regression. Defined as the tau parameter in the function rqss. A larger quantile yields a more stringent selection of HVG. Default is 0.7.

threshold

threshold of the normalized difference for HVG selection. Default is 3. A larger value results in a more stringent selection

plot.result

whether plot the selection results or not. Default is TRUE.

spline.df

the degree of freedom of the spline functions used to fit the quantile regression curve

Value

A list of elements:

score.mat

A score matrix of the genes. Each row is a gene

HVG.genes

A vector of the selected HVG gene names


jingshuw/descend documentation built on Sept. 2, 2018, 11:10 a.m.