build_10x_atac: Read in multiple 10X ATAC samples with Signac and merge with...

In BrianLohman/SingleCellGarage: A collection of utilities to make working with (and combining) existing single cell packages easier

Description

Takes file manifest from build_manifest following preffered merge procedure in Signac: https://satijalab.org/signac/articles/merging.html#merge-fragment-files-1

Usage

build_10x_atac(manifest = NULL, project = NULL)

Arguments

manifest	The file manifest from build_manifest or a list of named lists where each entry is a sample with peaks.bed, singlecell.csv and fragments
project	Name to give merged sample set

Details

"Fail to connect" or "Network is unreachable" errors are likely the result of a curl command reaching for the annotation but unable to connect to the server, possibly becuase of firewall issues. Try running the annotation block on a laptop outside of a firewall and then import the result back into the main notebook.

Examples

## Not run: 
srt = build_10X_atac(manifest = m, project = "A6440")

## End(Not run)

BrianLohman/SingleCellGarage documentation built on Feb. 24, 2022, 4:58 a.m.