Cytof2Seurat: function to convert cytof data into Seurat

In RyanYip-Kat/yipCat: Some function like ArchR style in Seurat Object

Description

function to convert cytof data into Seurat

Usage

Cytof2Seurat(
  sample_csv = NULL,
  config_csv = NULL,
  N = 20000,
  cofactor = 5,
  useFeatures = NULL,
  batch_correct = FALSE,
  batch_key = "sample",
  transformation = FALSE,
  path2barcode10X = "3M-february-2018.txt",
  outdir = "cytof"
)

Arguments

sample_csv	at least three columns(Path,Sample,Condition)
config_csv	at least two columns(channel(Cd111Di,Nd143Di...),marker(CD8A,CD11C..))
N	sample size,default sample 20000 each fcs file
useFeatures	feature names provide to run scaleData and runpca.
batch_correct	whether run batch correct to remove batch effect
batch_key	when remove batch correct,which key use to run.
transformation	whether transfrom data
path2barcode10X	10X barcode file,can be found in cellranger path

RyanYip-Kat/yipCat documentation built on Dec. 18, 2021, 11:55 a.m.