generateMeta: 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

generateMeta(
  dropletSCE = NULL,
  cellSCE = NULL,
  samplename,
  dir,
  HTAN = TRUE,
  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
dir	The output directory of the SCTK QC pipeline.
HTAN	Whether generates manifest file including HTAN specific ID (HTAN Biospecimen ID, HTAN parent file ID and HTAN patient ID). Default is TRUE.
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.