check_srtList: Check and preprocess a list of seurat objects

In zh542370159/SCP: Single Cell Pipeline

Check and preprocess a list of seurat objects

Description

This function checks and preprocesses a list of seurat objects. It performs various checks on the input, including verification of input types, assay type consistency, feature name consistency, and batch column consistency. It also performs data normalization and variable feature finding based on the specified parameters. Finally, it prepares the data for integration analysis based on the highly variable features.

Usage

check_srtList(
  srtList,
  batch,
  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

srtList	A list of Seurat objects to be checked and preprocessed.
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.

Value

A list containing the preprocessed seurat objects, the highly variable features, the assay name, and the type of assay (e.g., "RNA" or "Chromatin").

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