Find the marker genes the separate one cell type from all other cell types
postprocess_marker_variables.RdBased on the output of tiltedCCA::differential_expression, for a
particular cell type, 1) when comparing against every other cell type,
find all the variables that have an adjusted p-value
smaller than p_val_thres and also have a log fold change larger than
log_thres_name, and 2) if the variable was selected for more than
num_quantile_threshold percentage of the comparisons with other cell
types, we deem it as a marker gene for this cell type.
Usage
postprocess_marker_variables(
de_list,
log_thres_name = "avg_log2FC",
log_thres = 2,
num_quantile_threshold = 0.25,
p_val_name = "p_val",
p_val_adj_name = "p_val_adj",
p_val_thres = 1e-04
)Arguments
- de_list
output of the
tiltedCCA::differential_expressionfunction- log_thres_name
character of the column in each of
de_list$de_listfor the log fold change- log_thres
positive value, for selecting variables with log fold change larger than
log_thres- num_quantile_threshold
value between 0 and 1
- p_val_name
character of the column in each of
de_list$de_listfor the p-value- p_val_adj_name
character of the column in each of
de_list$de_listfor the multiple-testing adjusted p-value- p_val_thres
small positive value between 0 and 1, for selecting variables with p-values smaller than
p_val_thres