Add_Sample_Meta: Add Sample Level Meta Data

In samuel-marsh/scCustomize: Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing

Add Sample Level Meta Data

Description

Add meta data from ample level data.frame/tibble to cell level seurat ⁠@meta.data⁠ slot

Usage

Add_Sample_Meta(
  seurat_object,
  meta_data,
  join_by_seurat,
  join_by_meta,
  na_ok = FALSE,
  overwrite = FALSE
)

Arguments

seurat_object	object name.
meta_data	data.frame/tibble containing meta data or path to file to read. Must be formatted as either data.frame or tibble.
join_by_seurat	name of the column in [e-mail] that contains matching variables to join_by_meta in meta_data.
join_by_meta	name of the column in meta_data that contains matching variables to join_by_seurat in [e-mail].
na_ok	logical, is it ok to add NA values to [e-mail]. Default is FALSE. Be very careful if setting TRUE because if there is error in join operation it may result in all ⁠@meta.data⁠ values being replaced with NA.
overwrite	logical, if there are shared columns between [e-mail] and meta_data should the current [e-mail] columns be overwritten. Default is FALSE. This parameter excludes values provided to join_by_seurat and join_by_meta.

Value

Seurat object with new ⁠@meta.data⁠ columns

Examples

## Not run: 
# meta_data present in environment
sample_level_meta <- data.frame(...)
obj <- Add_Sample_Meta(seurat_object = obj, meta_data = sample_level_meta,
join_by_seurat = "orig.ident", join_by_meta = "sample_ID")

# from meta data file
obj <- Add_Sample_Meta(seurat_object = obj, meta_data = "meta_data/sample_level_meta.csv",
join_by_seurat = "orig.ident", join_by_meta = "sample_ID")

## End(Not run)

samuel-marsh/scCustomize documentation built on Dec. 20, 2024, 7:41 a.m.