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

Description Usage Arguments Value

View source: R/celltype.R

Description

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

Usage

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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


minzheguo/SINCERA documentation built on Feb. 3, 2021, 2:31 p.m.