check_srtMerge: Check and preprocess a merged seurat object

In zh542370159/SCP: Single Cell Pipeline

Check and preprocess a merged seurat object

Description

This function checks and preprocesses a merged seurat object.

Usage

check_srtMerge(
  srtMerge,
  batch = NULL,
  assay = NULL,
  do_normalization = NULL,
  normalization_method = "LogNormalize",
  do_HVF_finding = TRUE,
  HVF_source = "separate",
  HVF_method = "vst",
  nHVF = 2000,
  HVF_min_intersection = 1,
  HVF = NULL,
  vars_to_regress = NULL,
  seed = 11
)

Arguments

srtMerge	A merged Seurat object that includes the batch information.
batch	A character string specifying the batch variable name.
assay	The name of the assay to be used for downstream analysis.
do_normalization	A logical value indicating whether data normalization should be performed.
normalization_method	The normalization method to be used. Possible values are "LogNormalize", "SCT", and "TFIDF". Default is "LogNormalize".
do_HVF_finding	A logical value indicating whether highly variable feature (HVF) finding should be performed. Default is TRUE.
HVF_source	The source of highly variable features. Possible values are "global" and "separate". Default is "separate".
HVF_method	The method for selecting highly variable features. Default is "vst".
nHVF	The number of highly variable features to select. Default is 2000.
HVF_min_intersection	The feature needs to be present in batches for a minimum number of times in order to be considered as highly variable. The default value is 1.
HVF	A vector of highly variable features. Default is NULL.
vars_to_regress	A vector of variable names to include as additional regression variables. Default is NULL.
seed	An integer specifying the random seed for reproducibility. Default is 11.

See Also

check_srtList

zh542370159/SCP documentation built on Nov. 22, 2023, 2:34 a.m.