lvbsc: Low Variance Batch Spacing Correction (LVBSC)

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

Low Variance Batch Spacing Correction (LVBSC)

Description

This function takes an object of class scSeqR and finds the top genes with low variance across the samples to make a model for batch spacing correction.

Usage

lvbsc(x = NULL, dispersion.limit.max = 1.5, base.mean.rank = 500)

Arguments

x	An object of class scSeqR.
dispersion.limit.max	A number for taking the genes that have dispersion below 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.
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.
cell.transparency	Color transparency for the points in the plot, defult = 0.5.
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: 
lvbsc(my.obj,
               dispersion.limit.max = 1.5,
               base.mean.rank = 500,
               no.mito.model = T,
               mark.mito = T,
               interactive = T,
               out.name = "gene.model")

lvbsc(my.obj,
             dispersion.limit.max = 1.5,
             base.mean.rank = 500)

## End(Not run)

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