filterAtypicalExpressed: Filter samples with atypical expressoin data

In holgerman/HT12ProcessoR: Preprocessing Illuminas HT12 v4 data

Description

Filter samples for atypical gene expression levels. This is defined as atypical large Euclidian distance of all expressed, not batch-associated expression probes to an artificial individual. This artificial individual was defined as the average of samples after removing 10

Usage

filterAtypicalExpressed(
  ht12object,
  paramfile = NULL,
  filter2ind_atypischEuklid = "from_paramfile"
)

Arguments

ht12object	A list object of class HT12prepro created with function checkBatchEffects()
paramfile	Path to the file specifying parameters
filter2ind_atypischEuklid	Filter for extreme combination of values from expressed transcripts summarized as Euclidian distance of expression values of all expression probes previously classified as expressed and non-overinflated regarding ANOVA on batch-effects. Valid is ln('Euclidian distance') < median(ln('Euclidian Distance' )) + [value] * IQR(ln('Euclidian Distance' )). 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 '$chipsamples' is updated. Excluded individual are characterized by column in_study ==F and reason4exclusion. The slot with the history of the commands named '$history“ is updated.

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