filterLowExpressed: Filter samples with atypical number of expressed genes and...
In holgerman/HT12ProcessoR: Preprocessing Illuminas HT12 v4 data

This function filters from an HT12prepro object samples with atypical number of expressed genes and annotates probes for their respective expression level

filterLowExpressed(
  ht12object,
  paramfile = NULL,
  filter1ind_expressedGenes = "from_paramfile",
  filter1probes_expressedProbes = "from_paramfile"
)

`ht12object`	A list object of class HT12prepro created with function createExpressionSet()
`paramfile`	Path to the file specifying parameters.
`filter1ind_expressedGenes`	Filter for extreme number of 'Detected.Genes..0.01.' at detection p-value 0.01. Valid is: 'Detected.Genes..0.01.' < Median - [value]x IQR AND > Median - [value]x IQR. If "from_paramfile", than the parameter will be read from the paramfile with the location of this file given in parameter paramfile
`filter1probes_expressedProbes`	Attribute asigning an expression probe as 'expressed' if detected within at least [value]x n(individuals) at detection p-value 0.05. 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 '$chipsamples' is updated. Excluded individual are characterized by column in_study ==F and reason4exclusion. Additionally, a slot with the detailed probe-related expression level information named '$genesdetail is created, and the slot with the history of the commands named '$history“ is updated.

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