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Create a muscadet object

Source: R/objects.R
CreateMuscadetObject.Rd

Create a muscadet object.

Usage

CreateMuscadetObject(
  omics,
  bulk.lrr = NULL,
  bulk.label = NULL,
  genome = "hg38"
)

Arguments

omics

A list of muscomic objects (list). The names of the list will set the names of omics in the final object, if the list is unamed, the type is taken instead.

bulk.lrr

A data frame containing log R ratio per genomic segments from bulk sequencing data (data.frame). One row per segment and 4 columns ordered as followed: chromosome (integer), start position (integer), end position (integer), and Log R ratio value (numeric).

bulk.label

Label for bulk data (character string).

genome

Reference genome name among: "hg38", "hg19" and "mm10" (character string). "hg38" by default.

Value

A muscadet object.

Note

A muscadet object can contain several muscomic objects of the same type (ATAC or RNA for slot type) but they can't have identical labels (slot label.omic).

See also

Examples

# Create muscomic objects
atac <- CreateMuscomicObject(
  type = "ATAC",
  mat_counts = mat_counts_atac_tumor,
  allele_counts = allele_counts_atac_tumor,
  features = peaks
)
rna <- CreateMuscomicObject(
  type = "RNA",
  mat_counts = mat_counts_rna_tumor,
  allele_counts = allele_counts_rna_tumor,
  features = genes
)
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
)

# Create muscadet objects
muscadet <- CreateMuscadetObject(
  omics = list(atac, rna),
  bulk.lrr = bulk_lrr,
  bulk.label = "WGS",
  genome = "hg38"
)
muscadet_ref <- CreateMuscadetObject(
  omics = list(atac_ref, rna_ref),
  genome = "hg38"
)