CNV_htmp_glist: CNV_htmp_glist function

In alimahdipour/sciCNV: sciCNV

CNV_htmp_glist function

Description

Generates a heatmap of single cell CNV profiles plotted by gene list

Usage

CNV_htmp_glist(
  CNVmat,
  clustering = FALSE,
  clustering.type = c("pearson", "kendall", "spearman"),
  sorting = FALSE,
  CNVscore = NULL,
  cluster.lines = NULL,
  breakGlist,
  No.test
)

Arguments

CNVmat	copy number variation matrix
clustering	a TRUE/FALSE variable specifying whether to cluster cells based on their CNV similarities. Default is "FALSE"
Gen.Loc	Genomic Location matrix with list of genes, their associated chromosome numbers, starts and ends
clustering.type:	variable specifying the method that will be used to cluster sciCNV profiles (cells), if enabled. Possible options are "pearson", "euclidean", " spearman", ... "original" (retain the same cell order/clusters as original without further clustering). Default is "pearson". However this is only enabled when clustering = "TRUE"
sorting:	a TRUE/FALSE variable that enables sorting of cells based on their tumor CNV score from the largest to smallest tumor scores. Default is FASLE.
CNVscore:	the CNV score matrix for all cells (optionally divided by pre-determined clusters). Used only when sorting.clusters = TRUE.
cluster.lines:	is an optional list of values demarcating clusters of cells within the population; only used if multiple cell clusters exist beyond the simple division between test and control populations
breakGlist:	is a set of values each defines a vertical line that separates chromosomes
No.test:	the number of test cells included in the data; can be used to delineate distinct populations of of test annd control cells in the heatmap

Value

The output is the heatmap of sciCNV matrix for test and control cells against list of genes

Examples

CNVmat <- system.file("extdata", "Sample_CNV_matrix.txt", package="sciCNV")
breakGlist <- system.file("extdata", "Sample_breakGlist.txt", package ="sciCNV")
CNV_htmp_glist(CNVmat, breakGlist=breakGlist, sorting = FALSE,  No.test=20)

alimahdipour/sciCNV documentation built on Oct. 16, 2022, 12:56 p.m.