load.counts2 — load.counts2 • DEprot

Function used to generate a DEprot object starting from counts and metadata.

load.counts2(
  counts,
  metadata,
  data.type,
  log.base,
  normalization.method = NA,
  imputation.method = NA,
  column.id = "column.id"
)

Arguments

counts: A data.frame or a matrix in which the rownames are the proteins and the columns the samples.
metadata: A data.frame containing at least one column called column.id which corresponds to the colnames of counts. Any other column can be added and will correspond to a "feature"of each sample.
data.type: String indicating the type of data that are loaded. One among: 'raw', 'normalized', 'imputed'.
log.base: Number indicating the base of the log used to transform the counts. If none transformation is applied, indicate the base 1.
normalization.method: String or list indicating the normalization method used. If none, use the default value NA.
imputation.method: A string indicating the imputation method used. If none, use the default value NA.
column.id: String indicating the name of the column to use as "column.id" from the metadata data.frame. This column must contain all the colnames of counts.

A DEprot object (S4 vector).