load10X: Read data: raw to PCA
In ProfessionalFarmer/loonR: Common function in bioinformatics analysis

load10X

R Documentation

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,
  max_precent.hb = 10
)

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`	Default NULL. Specify detail DE method from SeuratWrappers::RunPrestoAll: e.g. wilcox_limma
`max_precent.hb`	Default 10