removeBatchEffects: Remove Batch effects from expressoin data of a HT12prepro...
In holgerman/HT12ProcessoR: Preprocessing Illuminas HT12 v4 data

This functions removes via ComBat from packge sva batch effects origniating from the Chip (Sentrix.Barcode) of the sample. If second_combat_withvar is provided, a second round of removeBatchEffects() is done.

removeBatchEffects(
  ht12object,
  paramfile = NULL,
  excludeERCC = "from_paramfile",
  save_subgroupcontrast = "from_paramfile",
  second_combat_withvar = "from_paramfile",
  additional_normalisation_after_combat = "from_paramfile",
  normalisation_method = "from_paramfile",
  showPlot_additional_normalisation_after_combat = T
)

`ht12object`	A list object of class HT12prepro created with function filter4MinBatchsize
`paramfile`	Path to the file specifying parameters
`excludeERCC`	exclude ERCC samples from following steps, this is suggested if some samples have spiked-in ERCC samples but others have not. If "from_paramfile", than the parameter will be read from the paramfile with the location of this file given in parameter paramfile.
`save_subgroupcontrast`	Protect the subgroup contrast (column subgroup in the table stored in the slot $chipsamples of the HT12prepro object)from beeing affected in batch ajdustment, CAVE risk of false positives when subgroups are unbalanced with batches, hence FALSE is in this case recommended. If "from_paramfile", than the parameter will be read from the paramfile with the location of this file given in parameter paramfile.
`second_combat_withvar`	A second round of removeBatchEffects() can be intended. In this case, batches from the first round checking Sentrix.Barcode batches as well as batches from this second round specified as a column in ht12object$chipsamples named according to this variable are removed sequentially. 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.
`additional_normalisation_after_combat`	Indicator (TRUE or FALSE), whether to normalize data after batch-correction with Combat using the normalization method specified in parameter 'normalisation_method'. If "from_paramfile", than the parameter will be read from the paramfile with the location of this file given in parameter paramfile.
`normalisation_method`	Method used for normalisation if parameter additional_normalisation_after_combat = TRUE. Either 'quantile' (quantile normalisation) or 'rsn' (robust spline normalisation). If "from_paramfile", than the parameter will be read from the paramfile with the location of this file given in parameter paramfile.

A list object of class HT12prepro where a slot with an expression set with normalized and transformed and batch-corrected data including control probe information is created. This slot is named '$total_nobkgd_eset_ql_combat'. Additionally, a graph is shown showing probe-wise as well as sample-wise correlation of expression data before and after batch adjustment.

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