specificity.criterion.selection: Determine the threshold for specificity filter based on a set...

In xu-lab/SINCERA: An R implementation of SINCERA pipeline for processing single-cell RNA-seq data.

Description

Determine the threshold for specificity filter based on a set of reference genes

Usage

specificity.criterion.selection(ES, group.by = SAMPLE.LABEL, groups = NULL,
  ref.idx = NULL, exp.t = 5, exp.p = 0.95, tolerance = 0.05,
  step = 0.1, do.plot = FALSE, verbose = T)

Arguments

ES	(ExpressionSet) an ExpressionSet object containing the single cell RNA-seq data
group.by	(character) the name of the column that contains the sample information
groups	(character) samples involves in determining the threshold
ref.idx	(numeric) a vectorcontaining the row indices of the set of reference genes
exp.t	(numeric) min expression value for the reference genes
exp.p	(numeric) min expression percentage per sample for the reference genes
tolerance	(numeric) percentage of reference genes that will be allowed to pass the specificity filters
step	(numeric) a numeric value between 0 and 1, specifying the granularity of
do.plot	(logical) plotting the distribution of specificity, the specificities of the reference genes (green lines), and the selected threshold (red line, if exists)
verbose	(logical) verbose the function output

Value

a numeric value between 0 and 1 if a threshold exists, otherwise, -1

xu-lab/SINCERA documentation built on Feb. 3, 2021, 4:19 a.m.