Description Usage Arguments Value
View source: R/filterLowExpressed.R
This function filters from an HT12prepro object samples with atypical number of expressed genes and annotates probes for their respective expression level
1 2 3 4 5 6 | 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.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.