writeAsymmetricMeltedChromosomalMatrixToDisk: Write a matrix, with genes, of a submatrix of a whole genome...

In CNVScope: A Versatile Toolkit for Copy Number Variation Relationship Data Analysis and Visualization

Write a matrix, with genes, of a submatrix of a whole genome interaction matrix to disk.

Description

Writes an RData file with a ggplot2 object within.

Usage

writeAsymmetricMeltedChromosomalMatrixToDisk(
  whole_genome_matrix,
  chrom1,
  chrom2,
  extra_data_matrix = NULL,
  transpose = F,
  sequential = T,
  debug = T,
  desired_range_start = 50,
  desired_range_end = 300,
  saveToDisk = T,
  max_cap = NULL,
  rescale = T
)

Arguments

whole_genome_matrix	A matrix to have edges averaged with genomic coordinates in the form chr1_50_100 set as the column and row names.
chrom1	first chromosome of the two which will subset the matrix. (this is done in row-column fasion).
chrom2	second chromosome of the two which will subset the matrix. (this is done in row-column fasion).
extra_data_matrix	A matrix with additional variables about each point, one position per row with as many variables as remaining columns.
transpose	transpose the matrix?
sequential	disable parallelization with registerDoSEQ()?
debug	extra output
desired_range_start	start of range for width and height of matrix for downsampling
desired_range_end	end of range for width and height of matrix for downsampling
saveToDisk	saves the matrix to disk
max_cap	maximum saturation cap, passed to signedRescale
rescale	perform signedRescale() on matrix?

Value

ggplotmatrix a matrix with values sufficient to create a ggplot2 heatmap with geom_tile() or with ggiraph's geom_tile_interactive()

Examples

load(system.file("extdata","grch37.rda",package = "CNVScope"))
load(system.file("extdata","nbl_result_matrix_sign_small.rda",package = "CNVScope"))
load(system.file("extdata","ensembl_gene_tx_table_prot.rda",package = "CNVScope"))
writeAsymmetricMeltedChromosomalMatrixToDisk(whole_genome_matrix = 
nbl_result_matrix_sign_small,
chrom1 = 1,chrom2 = 1,desired_range_start = 25, desired_range_end = 25)
file.remove("chr1_chr1_melted.RData")

CNVScope documentation built on March 31, 2022, 1:07 a.m.