determineBlobTypes: function that attempts to assign types and sizes to the blob...

In BenBruyneel/proteinDiscover: ProteinDiscover

function that attempts to assign types and sizes to the blob type columns in a table. The result from this function can be used in the dfTransformRaws function

Description

function that attempts to assign types and sizes to the blob type columns in a table. The result from this function can be used in the dfTransformRaws function

Usage

determineBlobTypes(
  theTable,
  minimumNumber = 1,
  numberOfGroups = minimumNumber,
  ratioNumberOfGroups = numberOfGroups - 1,
  blobDF = NA,
  specials = TRUE
)

Arguments

theTable	a data.frame with blob Columns (if no blobColumns are present, then NA is returned)
minimumNumber	this defines the minimum number of columns a blob/raw type column should be split into. In TMT10plex experiments, the minimumNumber will usually be 10, becauseyou have 10 channels/abundances
numberOfGroups	this defines how many 'groups' are present in the data. Taking Abundances as an example: Proteone Discoverer has both the original columns (say Abundances_1 through Abundances_2), but also columns where the abundances, that 'belong' together, are eg averaged or some other (statistical) measure is calculated over a number of columns. You may have eg 10 'Abundance channels' which are 5 samples total, each in duplo. This means that some columns in the resulting table will need to be split in 10 different columns (the original 'Abundances') while 'grouped' columns should be split into 5 different columns (eg the calculated means or variations of the 'abundances' columns). Note that although not enforced by the code, the numberOfGroups should always be equal or less than the minimumNumber parameter. Default value = minimumNumber
ratioNumberOfGroups	when ratios between groups are calculated we get columns (ratio columns) that need to be split into numberOfGroups - 1 (which is the efault value)
blobDF	essentially the result from either getBlobs; if NA then it will be generated by the getBlobs function with theTable as an argument
specials	default is TRUE, means that specials will be taken care of

Value

a data.frame with the name of the blob columns, their lengths, what (type) and minimumSize (number of variables in the blob)

Note

this function does not deal properly with specials, their types/ translations are resolved in a different way

there are two ways to see potential problems with the type assignments: the columns may contain NA values

BenBruyneel/proteinDiscover documentation built on March 16, 2024, 4:36 p.m.