Process a Seurat object (internal)

Normalize, find variable features, scale, and run PCA

Usage

ProcessSeuratObject(
  obj,
  normalization_method = "LogNormalize",
  scale_factor = 10000,
  scale_features = NULL,
  selection_method = "vst",
  verbose = TRUE
)

Arguments

obj

Seurat object

normalization_method

Normalization method ("LogNormalize", "CLR", or "RC")

scale_factor

Scaling factor for normalization

scale_features

Features to scale

selection_method

Variable feature selection method ("vst", "mvp", or "disp")

verbose

Print progress messages

Value

Seurat object

See also

Other single_cell_preprocess: ClusterAndReduce(), FilterTumorCell(), FindRobustElbow(), QCPatternFilter()