Identify Differentially Expressed Proteins

Usage

idep(
  df,
  id,
  clus_col,
  pval = 0.05,
  logf = 1,
  ex_col = NULL,
  prot_col = NULL,
  norm = TRUE
)

df: dataframe containing at least an ID-column and the proteins
id: string, the column name of the individual IDs
clus_col: string, column name containing the cluster membership
pval: numeric, adjusted p-value to filter on, default is 0.05
logf: numeric, log fold change to filter on, default is 1
ex_col: vector, names of other columns to exclude from the df, only required to exclude columns not specified in id or clus_col, or to exclude proteins specified in prot_col
prot_col: vector, names of the protein columns, if not specified, all columns not specified in id, clus_col, and ex_col will be assumed proteins
norm: boolean, whether normalisation should be applied, default is TRUE

a list of results

prot_col if the prot_col was not defined, it is listed here

lmfit result of lmFit

contr_fit results of contrasts.fit

bayes results of eBayes

toptable top results of the analysis

feptable differentially expressed protein results