return DEGs UP and DOWN list based on Rank Product

return DEGs UP and DOWN list based on Rank Product

DEGs_RP(
  tfit,
  lfc = NULL,
  p = 0.05,
  assemble = "intersect",
  Rank = "adj.P.Val",
  nperm = 1e+05,
  thres = 0.05,
  keep.top = NULL,
  keep.group = NULL,
  ...
)

Arguments

tfit

MArrayLM object generated by limma::treat()

lfc

num, cutoff of logFC for DE analysis

p

num, cutoff of p value for DE analysis

assemble

'intersect' or 'union', whether to select intersected or union genes of different comparisons, default 'intersect'

Rank

character, the variable for ranking DEGs, can be 'logFC', 'adj.P.Val'..., default 'adj.P.Val'

nperm

num, permutation runs of simulating the distribution

thres

num, cutoff for rank product permutation test if feature_selection = "rankproduct", default 0.05

keep.top

NULL or num, whether to keep top n DEGs of specific comparison

keep.group

NULL or pattern, specify the top DEGs of which comparison or group to be kept

...

omitted

Value

A list of "UP" and "DOWN" genes