generateHTANMeta: Generate HTAN manifest file for droplet and cell count data

In compbiomed/singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

Generate HTAN manifest file for droplet and cell count data

Description

Generate HTAN manifest file for droplet and cell count data

Usage

generateHTANMeta(
  dropletSCE = NULL,
  cellSCE = NULL,
  samplename,
  htan_biospecimen_id,
  dir,
  dataType = c("Droplet", "Cell", "Both")
)

Arguments

dropletSCE	A SingleCellExperiment object containing droplet count matrix data
cellSCE	A SingleCellExperiment object containing cell count matrix data
samplename	The sample name of the SingleCellExperiment objects
htan_biospecimen_id	The HTAN biospecimen id of the sample in SingleCellExperiment object
dir	The output directory of the SCTK QC pipeline.
dataType	Type of the input data. It can be one of "Droplet", "Cell" or "Both".

Value

A SingleCellExperiment object which combines all objects in sceList. The colData is merged.

compbiomed/singleCellTK documentation built on Feb. 10, 2024, 3:32 a.m.