load10X: Read data: raw to PCA

In ProfessionalFarmer/loonR: Common function in bioinformatics analysis

Read data: raw to PCA

Description

Read data: raw to PCA

Usage

load10X(
  paths = NA,
  sample_names = NA,
  min.cells = 10,
  min.features = 200,
  gene.column = 1,
  remove_doublet = T,
  batch = NULL,
  max_nCount_RNA = 10000,
  max_nFeature_RNA = 8000,
  max_percent.mt = 20,
  integrate_CCA = FALSE,
  top_variable_features = 2000,
  remove_cc = T,
  remove_mt = F,
  integrate_harmony = F,
  harmony_batch_colName = "orig.ident",
  find_marker = NULL,
  dims = 1:30
)

Arguments

min.cells	10
min.features	200
gene.column	1
batch	Default 1
max_nFeature_RNA	8000
max_percent.mt	20
integrate_CCA	Default FALSE
top_variable_features	2000
harmony_batch_colName	Column names from batch correction
find_marker	Specify detail DE method: e.g. wilcox_limma

Value

res

ProfessionalFarmer/loonR documentation built on Oct. 9, 2024, 9:56 p.m.