View source: R/variable_genes.R
calculateHVF | R Documentation |
compute highly variable features
calculateHVF(
gobject,
spat_unit = NULL,
feat_type = NULL,
expression_values = c("normalized", "scaled", "custom"),
method = c("cov_groups", "cov_loess", "var_p_resid"),
reverse_log_scale = FALSE,
logbase = 2,
expression_threshold = 0,
nr_expression_groups = 20,
zscore_threshold = 1.5,
HVFname = "hvf",
difference_in_cov = 0.1,
var_threshold = 1.5,
var_number = NULL,
show_plot = NA,
return_plot = NA,
save_plot = NA,
save_param = list(),
default_save_name = "HVFplot",
return_gobject = TRUE
)
gobject |
giotto object |
spat_unit |
spatial unit |
feat_type |
feature type |
expression_values |
expression values to use |
method |
method to calculate highly variable features |
reverse_log_scale |
reverse log-scale of expression values (default = FALSE) |
logbase |
if reverse_log_scale is TRUE, which log base was used? |
expression_threshold |
expression threshold to consider a gene detected |
nr_expression_groups |
[cov_groups] number of expression groups for cov_groups |
zscore_threshold |
[cov_groups] zscore to select hvg for cov_groups |
HVFname |
name for highly variable features in cell metadata |
difference_in_cov |
[cov_loess] minimum difference in coefficient of variance required |
var_threshold |
[var_p_resid] variance threshold for features for var_p_resid method |
var_number |
[var_p_resid] number of top variance features for var_p_resid method |
show_plot |
show plot |
return_plot |
return ggplot object |
save_plot |
directly save the plot [boolean] |
save_param |
list of saving parameters from |
default_save_name |
default save name for saving, don't change, change save_name in save_param |
return_gobject |
boolean: return giotto object (default = TRUE) |
Currently we provide 2 ways to calculate highly variable genes:
1. high coeff of variance (COV) within groups:
First genes are binned (nr_expression_groups) into average expression groups and
the COV for each feature is converted into a z-score within each bin. Features with a z-score
higher than the threshold (zscore_threshold) are considered highly variable.
2. high COV based on loess regression prediction:
A predicted COV is calculated for each feature using loess regression (COV~log(mean expression))
Features that show a higher than predicted COV (difference_in_cov) are considered highly variable.
giotto object highly variable features appended to feature metadata (fDataDT)
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