make.gene.model: Make a gene model for clustering

In rezakj/scSeqR: scSeqR; a toolkit to analyze single cell sequencing data types (i.e scRNA-seq) and large numeric matrix files.

Make a gene model for clustering

Description

This function takes an object of class scSeqR and priveds a gene list for clustering based on the parameters set in the model.

Usage

make.gene.model(x = NULL, dispersion.limit = 1.5,
  base.mean.rank = 500, non.sig.col = "darkgray",
  right.sig.col = "chartreuse3", left.sig.col = "cadetblue3",
  disp.line.col = "black", rank.line.col = "red", cell.size = 1.75,
  cell.transparency = 0.5, no.mito.model = T, no.cell.cycle = T,
  mark.mito = T, interactive = TRUE, out.name = "plot")

Arguments

x	An object of class scSeqR.
dispersion.limit	A number for taking the genes that have dispersion above this number, defult = 1.5.
base.mean.rank	A number taking the top genes ranked by base mean, defult = 500.
non.sig.col	Color for the genes not used for the model, defult = "darkgray".
right.sig.col	Color for the genes above the dispersion limit, defult = "chartreuse3".
left.sig.col	Color for the genes above the rank limit, defult = "cadetblue3".
disp.line.col	Color of the line for dispersion limit, defult = "black".
rank.line.col	Color of the line for rank limit, defult = "red".
cell.size	A number for the size of the points in the plot, defult = 1.75.
cell.transparency	Color transparency for the points in the plot, defult = 0.5.
no.mito.model	If set to TRUE, mitochondrial genes would be excluded from the gene list made for clustering, defult = TRUE.
mark.mito	Mark mitochondrial genes in the plot, defult = TRUE.
interactive	If set to TRUE an intractive HTML file will be created, defult = TRUE.
out.name	If "interactive" is set to TRUE, the out put name for HTML, defult = "plot".

Value

An object of class scSeqR.

Examples

## Not run: 
make.gene.model(my.obj,
               dispersion.limit = 1.5,
               base.mean.rank = 500,
               no.mito.model = T,
               mark.mito = T,
               interactive = T,
               out.name = "gene.model")

make.gene.model(my.obj,
             dispersion.limit = 1.5,
             base.mean.rank = 500,
             no.mito.model = T,
             mark.mito = T,
             interactive = F,
             out.name = "gene.model")

## End(Not run)

rezakj/scSeqR documentation built on March 28, 2022, 12:17 p.m.