filter_genes {CEMiTool} | R Documentation |
Filter a gene expression data.frame
filter_genes(expr, pct = 0.75, apply_vst = FALSE)
expr |
A data.frame containing expression data |
pct |
Percentage of most expressed genes to keep. |
apply_vst |
Logical. If TRUE, will apply variance stabilizing transform before filtering data. |
This function takes a gene expression data.frame and applies a
percentage filter (keeps the pct
) most expressed genes). If
apply_vst
is TRUE, a variance stabilizing transformation is applied on
gene expression values as long as mean and variance values have a Spearman's
rho of over 0.5. This transformation is intended to remove this dependence
between the parameters. One should then apply the select_genes
function to get significant genes.
A data.frame containing filtered expression data
# Get example expression data data(expr0) # Filter genes expr_f <- filter_genes(expr0) # Check selected genes expr_f[1:5, 1:5] # Filter genes and apply variance stabilizing transformation expr_f2 <- filter_genes(expr0, apply_vst=TRUE) # Check results expr_f2[1:5, 1:5] # Selected genes selected <- select_genes(expr_f2) # Get data.frame with only selected genes expr_s <- expr_f2[selected, ] # Check results expr_s[1:5, 1:5]