Create a muscomic object

Create a muscomic object.

Usage

CreateMuscomicObject(
  type = c("ATAC", "RNA"),
  mat_counts,
  features,
  allele_counts = NULL,
  label.omic = NULL,
  label.features = NULL
)

Arguments

type

Type of single cell omic, either "ATAC" or "RNA" (character string).

mat_counts

Matrix of raw counts features x cells (matrix or dgCMatrix). Rows are features (they must correspond to the id column of features), and columns are cells.

features

Data frame of features (peaks, genes...) coordinates on genome (data.frame). It should contain 4 columns:

CHROM

Chromosome names in character format, e.g. "15", "X" (character).

start

Start positions (integer).

end

End positions (integer).

id

Unique identifiers, e.g. gene name "CDH1" or peak identifier CHROM_start_end "1_1600338_1600838" (character). It should match the feature identifiers as row names of mat_counts.

allele_counts

Data frame of allele counts at variant positions per cell (data.frame). Variant positions can be either common single nucleotide polymorphisms (SNPs) positions or individual-specific heterozygous positions retrieved from bulk sequencing. The data frame format is based on the Variant Calling Format (VCF), thereby it must contain the following columns : cell, id, CHROM, POS, REF, ALT, RD, AD, DP, (GT). See allele_counts() for details.

label.omic

Label for the single cell omic (character string). By default "scATAC-seq" is used for "ATAC" type and "scRNA-seq" for "RNA" type.

label.features

Label for features (character string). By default "peaks" is used for "ATAC" type and "genes" for "RNA" type.

Value

A muscomic object.

See also

• CreateMuscadetObject()

• muscomic, muscadet

Examples

atac <- CreateMuscomicObject(
  type = "ATAC",
  mat_counts = mat_counts_atac_tumor,
  allele_counts = allele_counts_atac_tumor,
  features = peaks
)
atac
#> A muscomic object of type ATAC labelled scATAC-seq containing: 
#>  mat.counts coverage data matrix 
#>  112 cells 
#>  1000 features: peaks 
#>  691 variant positions 

rna <- CreateMuscomicObject(
  type = "RNA",
  mat_counts = mat_counts_rna_tumor,
  allele_counts = allele_counts_rna_tumor,
  features = genes
)
rna
#> A muscomic object of type RNA labelled scRNA-seq containing: 
#>  mat.counts coverage data matrix 
#>  119 cells 
#>  500 features: genes 
#>  373 variant positions 

atac_ref <- CreateMuscomicObject(
  type = "ATAC",
  mat_counts = mat_counts_atac_ref,
  allele_counts = allele_counts_atac_ref,
  features = peaks
)

rna_ref <- CreateMuscomicObject(
  type = "RNA",
  mat_counts = mat_counts_rna_ref,
  allele_counts = allele_counts_rna_ref,
  features = genes
)
rna_ref
#> A muscomic object of type RNA labelled scRNA-seq containing: 
#>  mat.counts coverage data matrix 
#>  97 cells 
#>  500 features: genes 
#>  373 variant positions 

# without allele counts data (not required for clustering step)
atac2 <- CreateMuscomicObject(
  type = "ATAC",
  mat_counts = mat_counts_atac_tumor,
  features = peaks
)
atac2
#> A muscomic object of type ATAC labelled scATAC-seq containing: 
#>  mat.counts coverage data matrix 
#>  112 cells 
#>  1000 features: peaks 
#>  0 variant positions