filter4MinBatchsize: Filter samples of a HT12prepro object for min batch size n>1

In holgerman/HT12ProcessoR: Preprocessing Illuminas HT12 v4 data

Description

This functions filters for min Batch size n>1 as this is a limitation for following removal of batch effects in the following step applying function removeBatchEffects()

Usage

filter4MinBatchsize(
  ht12object,
  paramfile = NULL,
  second_combat_withvar = "from_paramfile"
)

Arguments

ht12object	A list object of class HT12prepro created with function filterTechnicallyFailed()
paramfile	Path to the file specifying parameters
second_combat_withvar	A second round of removeBatchEffects() can be intended. In this case, batches from the first round checking Sentrix.Barcode batches as well as batches from this second round specified as a column in ht12object$chipsamples named according to this variable must be checked for minimum batch size n>1.If "", no 2nd combat will be done. If "from_paramfile", than the parameter will be read from the paramfile with the location of this file given in parameter paramfile.

Value

A list object of class HT12prepro where the slot with sample-related attributes of the current processing-stage named '$chipsamples' is update. Excluded individual are characterized by column in_study ==F and reason4exclusion

holgerman/HT12ProcessoR documentation built on June 5, 2021, 9:18 a.m.