Construct iEDGE input object

construct_iEDGE(cn, gep, cisgenes, transgenes = NA, cn.fdat, gep.fdat,
  cn.pdat = NA, gep.pdat = NA)

Arguments

cn

matrix of epi-DNA alterations (m rows of alterations by n samples)

gep

matrix of gene expression (g rows of genes by n samples)

cisgenes

list of cis genes corresponding to each row in cn

transgenes

optional list of trans genes corresponding to each row in cn

cn.fdat

data frame of row annotations for cn, must have column of row identifiers, and optionally column of direction identifiers if one-sided DE tests are applied

gep.fdat

data frame of row annotaions for gep, must have column of row identifiers

cn.pdat

optional data frame of column annotations for cn

gep.pdat

optional data frame of column annotations for gep