normalize.counts

Function that allows for the tail-robust quantile normalization of the counts using the MBQN package.

normalize.counts(
  DEprot.object,
  balancing.function = "median",
  NRI.RI.ratio.threshold = 0.5,
  overwrite.normalization = FALSE
)

Arguments

DEprot.object

A DEprot object, as generated by load.counts.

balancing.function

A string indicating the function to use to balance the quantile normalization. Default: "median".

NRI.RI.ratio.threshold

Value indicating the NRI/RI (nearly rank invariant (NRI)/rank invariant (RI)) ratio threshold. Default: 0.5.

overwrite.normalization

Logical value to indicate whether, in the case already available, the table of normalized counts should be overwritten. Default: FALSE.

Value

A DEprot object. A boxplot showing the distribution of the protein intensity after normalization for each sample is added to the slot (boxplot.norm).

See also

load.counts, MBQN package.

Author

Sebastian Gregoricchio

Examples

normalize.counts(DEprot.object = DEprot::test.toolbox$dpo.raw)
#> DEprot object:
#>            Samples:  12
#>           Proteins:  50
#>   Counts available:  raw, normalized
#> Log transformation:  log2
#>   Metadata columns:  column.id, sample.id, cell, condition, combined.id, replicate