CNV_htmp_gloc: CNV_htmp_gloc function

In alimahdipour/sciCNV: sciCNV

CNV_htmp_gloc function

Description

Generates heatmap of sciCNV profiles, plotted by Genomic location (gloc)

Usage

CNV_htmp_gloc(
  CNVmat,
  clustering = FALSE,
  clustering.type = NA,
  sorting = TRUE,
  CNVscore = NULL,
  cluster.lines = NULL,
  breakGloc,
  No.test
)

Arguments

CNVmat	copy number variation matrix
clustering	TRUE/FALSE variable specifying whether to cluster cells based on their CNV similarities. Default is "FALSE"
clustering.type	Variable specifying the clustering method to be used in generating the heatmap. Possible options are "pearson", "euclidean", " spearman", ... "original" (retains the original cell order without unsupervised clustering). Default is "pearson". Only enabled when clustering = "TRUE"
sorting	TRUE/FALSE variable specifying whether to sort cells based on their tumor CNV score from the largest to smallest tumor scores. Default is FALSE.
CNVscore	is the tumor CNV score matrix for all cells (possibly ranked within clusters). Only used when sorting.clusters = TRUE.
cluster.lines	is a list of values which can be used to separate cell clusters within the population; only used if multiple clusters present
breakGloc	is a set of values each defines a vertical line that separates chromosomes
No.test	number of test cells included in the data; can be used to delineate the populations of test and control cells in the heatmap

Value

The output is the heatmap of sciCNV matrix for test and control cells against genomic location

Note

Please refer to the reference and supplemental materials described in the README for additional details.

Author(s)

Ali Mahdipour-Shirayeh, Princess Margaret Cancer Centre, University of Toronto

Examples

CNVmat <- system.file("extdata", "Sample_CNV_matrix.txt", package="sciCNV")
breakGloc <- system.file("extdata", "Sample_breakGloc.txt", package = "sciCNV")
CNV_htmp_gloc(CNVmat, breakGloc=breakGloc, sorting = FALSE,  No.test=20)

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