make_new_container {scITD}

Create a container to store all data and results for the project. You must provide a params list as generated by initialize_params(). You also need to provide either a Seurat object or both a count_data matrix and a meta_data matrix.

Description

Create a container to store all data and results for the project. You must provide a params list as generated by initialize_params(). You also need to provide either a Seurat object or both a count_data matrix and a meta_data matrix.

Usage

make_new_container(
  params,
  count_data = NULL,
  meta_data = NULL,
  seurat_obj = NULL,
  scMinimal = NULL,
  gn_convert = NULL,
  metadata_cols = NULL,
  metadata_col_nm = NULL,
  label_donor_sex = FALSE
)

Arguments

params

list A list of the experiment params to use as generated by initialize_params()

count_data

dgCMatrix Matrix of raw counts with genes as rows and cells as columns (default=NULL)

meta_data

data.frame Metadata with cells as rows and variables as columns. Number of rows in metadata should equal number of columns in count matrix (default=NULL)

seurat_obj

Seurat object that has been cleaned and includes the normalized, log-transformed counts. The meta.data should include a column with the header 'sex' and values of 'M' or 'F' if available. The metadata should also have a column with the header 'ctypes' with the corresponding names of the cell types as well as a column with header 'donors' that contains identifiers for each donor. (default=NULL)

scMinimal

environment A sub-container for the project typically consisting of gene expression data in its raw and processed forms as well as metadata (default=NULL)

gn_convert

data.frame Gene identifier -> gene name conversions table. Gene identifiers used in counts matrices should appear in the first column and the corresponding gene symbols should appear in the second column. Can remain NULL if the identifiers are already gene symbols. (default=NULL)

metadata_cols

character The names of the metadata columns to use (default=NULL)

metadata_col_nm

character New names for the selected metadata columns if wish to change their names. If NULL, then the preexisting column names are used. (default=NULL)

label_donor_sex

logical Set to TRUE to label donor sex in the meta data by using expressing of sex-associated genes (default=FALSE)

Value

A project container of class environment that stores sub-containers for each cell type as well as results and plots from all analyses.