return DGEList containing vfit by limma::voom (if normalize = TRUE) and tfit by limma::treat

return DGEList containing vfit by limma::voom (if normalize = TRUE) and tfit by limma::treat

voom_fit_treat(
  dge,
  group_col,
  target_group,
  normalize = TRUE,
  group = FALSE,
  lfc = 0,
  p = 0.05,
  batch = NULL,
  summary = TRUE,
  ...
)

Arguments

dge

DGEList object for DE analysis, including expr and samples info

group_col

character, column name of coldata to specify the DE comparisons

target_group

pattern, specify the group of interest, e.g. NK

normalize

logical, if the expr in data is raw counts needs to be normalized

group

logical, TRUE to separate samples into only 2 groups: `target_group`` and 'Others'; FALSE to set each level as a group

lfc

num, cutoff of logFC for DE analysis

p

num, cutoff of p value for DE analysis and permutation test if feature_selection = "rankproduct"

batch

vector of character, column name(s) of coldata to be treated as batch effect factor, default NULL

summary

logical, if to show the summary of DE analysis

...

omitted

Value

A DGEList containing vfit and tfit