training_set: K-caller (Training Set; EUR, Illumina Infinium...
In BenjaminPlanterose/UMtools: An R-package for analysing Illumina DNA Methylation arrays at the fluorescence intensity level
training_set R Documentation
K-caller (Training Set; EUR, Illumina Infinium HumanMethylation450 Beadchip microarray)
Description
Includes a list 4 vectors of 450K cg id's:
K = 1
K = 2
K = 3
K = 4
These correspond to probes that form from 1 to 4 clusters in the U/M plane on a dataset of
426 MZ twin pairs of the E-risk cohort (British, EUR ancestry). These sets were compiled
by manually examining U/M plots of random probes. However, the number of clusters observed
may be different in other datasets. Key parameters that will determine if this is true
will be sample size or ancestry.
If one manually verifies that these lists apply to their own dataset, they can be used for
calibrating parameters eps and minPts from the K-caller.
Usage
data(training_set)
Format
An object of class list
References
Revisiting Genetic artefacts on DNA methylation microarrays. Genome Research
Examples
data(training_set)
BenjaminPlanterose/UMtools documentation built on Aug. 19, 2024, 4:54 a.m.
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| training_set | R Documentation |
K-caller (Training Set; EUR, Illumina Infinium HumanMethylation450 Beadchip microarray)
Description
Includes a list 4 vectors of 450K cg id's:
K = 1
K = 2
K = 3
K = 4
These correspond to probes that form from 1 to 4 clusters in the U/M plane on a dataset of 426 MZ twin pairs of the E-risk cohort (British, EUR ancestry). These sets were compiled by manually examining U/M plots of random probes. However, the number of clusters observed may be different in other datasets. Key parameters that will determine if this is true will be sample size or ancestry. If one manually verifies that these lists apply to their own dataset, they can be used for calibrating parameters eps and minPts from the K-caller.
Usage
data(training_set)
Format
An object of class list
References
Revisiting Genetic artefacts on DNA methylation microarrays. Genome Research
Examples
data(training_set)
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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