slidingJaccard: Plot two functional annotation charts using a sliding Jaccard...
In sam-bassett/CompGO: An R pipeline for .bed file annotation, comparing GO term enrichment between gene sets and data visualisation
Description
Usage
Arguments
Examples
Description
This function compares two functional annotation charts using a sliding Jaccard coefficient - a ranked list of P-values is produced, and a sliding window is used to find the Jaccard coefficient of two charts at different cutoffs of the top n terms. This is useful to determine where the majority of overlapping terms is located, and can also be used to compare Jaccard profiles between multiple (up to 4) sets if C and D are supplied.
Usage
1
slidingJaccard(setA, setB, increment = 50, setC = NULL, setD = NULL)
Arguments
setA
A DAVIDFunctionalAnnotationChart to compare
setB
A DAVIDFunctionalAnnotationChart to compare
increment
The number of terms (n) to increment for each sliding window
setC
A DAVIDFunctionalAnnotationChart to compare, optional
setD
A DAVIDFunctionalAnnotationChart to compare, optional
Examples
1
2
3
data(funChart1)
data(funChart2)
slidingJaccard(funChart1, funChart2, 50, FALSE)
sam-bassett/CompGO documentation built on May 29, 2019, 1:01 p.m.
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Description Usage Arguments Examples
Description
This function compares two functional annotation charts using a sliding Jaccard coefficient - a ranked list of P-values is produced, and a sliding window is used to find the Jaccard coefficient of two charts at different cutoffs of the top n terms. This is useful to determine where the majority of overlapping terms is located, and can also be used to compare Jaccard profiles between multiple (up to 4) sets if C and D are supplied.
Usage
1 | slidingJaccard(setA, setB, increment = 50, setC = NULL, setD = NULL)
|
Arguments
setA |
A DAVIDFunctionalAnnotationChart to compare |
setB |
A DAVIDFunctionalAnnotationChart to compare |
increment |
The number of terms (n) to increment for each sliding window |
setC |
A DAVIDFunctionalAnnotationChart to compare, optional |
setD |
A DAVIDFunctionalAnnotationChart to compare, optional |
Examples
1 2 3 | data(funChart1)
data(funChart2)
slidingJaccard(funChart1, funChart2, 50, FALSE)
|
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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