Expression matrix normalization method.
Steps:
Total library size normalization and scaling by a custom scale-factor.
Log transformation of data.
library_size_norm | logical (default = TRUE). whether to perform
library size normalization |
scalefactor | numeric (default = 6000). Scalefactor to use after
library size normalization. (skipped if library_size_norm = FALSE) |
log_norm | logical (default = TRUE). Whether to transform values to
log-scale. |
log_offset | numeric (default = 1). If log_norm = TRUE, offset
value to add to expression values to avoid log(0) |
logbase | numeric (default = 2). If log_norm = TRUE, log base to
use to log normalize expression values |
Other normalization parameters:
norm_arcsinh,
norm_l2,
norm_library,
norm_log,
norm_osmfish,
norm_pearson,
norm_quantile,
norm_tfidf