Description Usage Arguments Value
View source: R/filterAtypicalExpressed.R
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
1 2 3 4 5 | filterAtypicalExpressed(
ht12object,
paramfile = NULL,
filter2ind_atypischEuklid = "from_paramfile"
)
|
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. |
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.
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