read_loom_and_analyze: Read and process loom and H5AD files from FlyCellAtlas

In ipatop/FlyCellAtlas.download.with.annotations: Reads and process loom files from FlyCellAtlas to be compatible with Seurat

Read and process loom and H5AD files from FlyCellAtlas

Description

This function requires loom and h5ad files from FlyCellAtlas and process them into Seurat objects. It then also re-analyze them to get the full gene-expression matrix and not only the extract marker genes and also get further information.

Usage

read_loom_and_analyze(
  loom_file = "./loom/s_fca_biohub_body_wall_10x.loom",
  h5ad_file = "./loom/s_fca_biohub_body_wall_10x.h5ad",
  plot = T,
  dir = "./"
)

Arguments

loom_file	character with Name and directory of loom file
h5ad_file	character with Name and directory of h5da file
plot	Boolean indicating if plots should be generated
dir	Directory to save RData and plots in

Value

It saves old and new Seurat onjects along with marker genes and metadata. *"_h5" is seurat object from the paper, this only has most variable genes

*"_new" is the new seurat object

*"_new_markers" is all.marker genes from the new seurat object with all genes

*"_paper_markers" is all.marker genes from the paper

*,"_matadata" is the metadata

Examples

There are examples in the folder names "./loom". To run it:
read_loom_and_analyze(loom_file = "~/Documents/scripts/FlyCellAtlas_download_with_annotations/loom/s_fca_biohub_body_wall_10x.loom")

ipatop/FlyCellAtlas.download.with.annotations documentation built on March 26, 2022, 1:46 a.m.