Extract data from Seurat object

Extract data from Seurat object

Usage

extractFromSeurat(
  seurat_obj,
  features = NULL,
  assay_name = "RNA",
  slot_name = "counts",
  indiv_colname = "indiv",
  ...
)

Arguments

seurat_obj

a Seurat object

features

string vector to filter for features

assay_name

string scalar to specify the name of input assay data

slot_name

string scalar to specify the type of input assay data

indiv_colname

string scalar to specify the column that has the indiv ids

...

other options to specify extracted outputs. Currently available:

• col_class : logical value

• feat_names : logical value

• cell_names : logical value

• sc_indiv : logical value

• expr_mat : logical value

• sc_cov : logical value

• feat_cov : logical value

Value

a list of extracted data with following optional outputs:

• col_class : a vector of the column classes for cell covariate variables

• feat_names : a vector of feature names

• cell_names : a vector of cell names

• sc_indiv : a vector of distinct sample ids extracted from cell covariate using indiv_colname

• expr_mat : an expression matrix extracted using assay_name and slot_name options

• sc_cov : a dataframe for cell covariates

• feat_cov : a dataframe for feature covariates

Examples

NULL
#> NULL