filter_expr {CEMiTool} | R Documentation |
Filter gene expression table
filter_expr(cem, ...) ## S4 method for signature 'CEMiTool' filter_expr(cem, filter_pval = 0.1, n_genes, pct = 0.75, apply_vst = FALSE)
cem |
Object of class |
... |
Optional parameters. |
filter_pval |
P-value cutoff for gene selection. |
n_genes |
Number of genes to be selected. |
pct |
Percentage of most expressed genes to keep (before variance filter). |
apply_vst |
Logical. If TRUE, will apply variance stabilizing transform before filtering data. |
Object of class CEMiTool
with selected genes
# Get example expression data data(expr0) # Initialize CEMiTool object with expression cem <- new_cem(expr0) # Filter genes cem1 <- filter_expr(cem) # Check selected genes head(expr_data(cem1)) # Filter genes and apply variance stabilizing transformation cem2 <- filter_expr(cem, apply_vst=TRUE) # Check results head(expr_data(cem2))