OmicsProfiles

profile.png
AnnotatedProfile supports multi-omics data with respect to the same set of cells, while OmicsProfile holds single omic data with layers which contains data with the same set of features.
OmicsProfiles.Profile — Function
Profile(countmat, omicsname, var, obs; varindex=:genesymbol, obsindex::Symbol=:barcode,
        T=float(eltype(countmat)))

Constructor for establishing AnnotatedProfile with a OmicsProfile inside.

Arguments

  • countmat: The count matrix for given omics and it will be set to key :count.
  • omicsname::Symbol: The name of given OmicsProfile.
  • var::DataFrame: The dataframe contains meta information for features or variables.
  • obs::DataFrame: The dataframe contains meta information for observations.
  • varindex::Symbol: The index of dataframe var.
  • obsindex::Symbol: The index of dataframe obs.
  • T: Element type of countmat.
OmicsProfiles.OmicsProfile — Type
OmicsProfile(countmat, var, varindex; T=float(eltype(countmat)))

Arguments

  • countmat: The count matrix for given omics and it will be set to key :count.
  • var::DataFrame: The dataframe contains meta information for features or variables.
  • varindex::Symbol: The index of dataframe var.
  • T: Element type of countmat.

Examples

julia> r, c = (100, 500)
(100, 500)

julia> data = rand(0:100, r, c);

julia> var = DataFrame(index=1:r, C=rand(r), D=rand(r));

julia> prof = OmicsProfile(data, var, :index)
OmicsProfile (nvar = 100):
    var: index, C, D
    layers: count
OmicsProfiles.AnnotatedProfile — Type
AnnotatedProfile(omics, obs, obsindex)
AnnotatedProfile(op, omicsname, obs, obsindex)

Arguments

  • omics::Dict{Symbol,OmicsProfile}: A collection of omics profile with their names in keys.
  • op::OmicsProfile: Single omics profile.
  • omicsname::Symbol: The name of given OmicsProfile.
  • obs::DataFrame: The dataframe contains meta information for observations.
  • obsindex::Symbol: The index of dataframe obs.
OmicsProfiles.read_10x — Function
read_10x(path; make_unique=true, omicsname=:RNA, varnames=[:ensembleid, :genesymbol],
    obsnames=[:barcode], varindex=:genesymbol, obsindex=:barcode)

Reads 10x dataset from path and returns an AnnotatedProfile.

Arguments

  • path::AbstractString: The path to 10x dataset folder.
  • make_unique::Bool: To make varindex unique or not if given varindex is not unique.
  • omicsname::Symbol: The name of given sequencing data.
  • varnames::AbstractVector: The header or column names of feature file.
  • obsnames::AbstractVector: The header or column names of barcode file.
  • varindex::Symbol: The index of dataframe var.
  • obsindex::Symbol: The index of dataframe obs.

Examples

julia> using SnowyOwl

julia> prof = read_10x(SnowyOwl.Dataset.pbmc3k_folder(), varindex=:ensembleid)
AnnotatedProfile (nobs = 2700):
    obs: barcode
RNA => OmicsProfile (nvar = 32738):
    var: ensembleid, genesymbol
    layers: count