Description Usage Arguments Value Examples
View source: R/confounders_clsq_class.R
Univariate least squares regression models are used to compare models with and without potential confounding factors included. The change in coefficients (delta) is then computed for each potential confounding factor. Factors with a large delta are said to be having a large impact on the model and are therefore confounding. p-values are computed for models with confounders included to reduce potential false positives. Only suitable for main factors with 2 levels.
1 2 3 4 5 6 7 8 | confounders_clsq(
alpha = 0.05,
mtc = "fdr",
factor_name,
confounding_factors,
threshold = 0.15,
...
)
|
alpha |
(numeric) The p-value cutoff for determining significance. The default is |
mtc |
(character) Multiple test correction method. Allowed values are limited to the following:
The default is |
factor_name |
(character) The name of the main factor with which other factors may be confounding. |
confounding_factors |
(character) The name(s) of factor(s) that are potential confounding factors. |
threshold |
(numeric) Factors with a delta greater than the the threshold are considered to be confounding. The default is |
... |
Additional slots and values passed to |
A confounders_clsq
object.
1 2 3 4 5 6 7 8 | D = MTBLS79_DatasetExperiment()
M = filter_by_name(mode='include',dimension='variable',
names=colnames(D$data)[1:10]) + # first 10 features
filter_smeta(mode='exclude',levels='QC',
factor_name='class') + # reduce to two group comparison
confounders_clsq(factor_name = 'class',
confounding_factors=c('sample_order','batch'))
M = model_apply(M,D)
|
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