gaiaCNVplot: Creates a plot for GAIA output (all significant aberrant...
In daniel615212950/TCGAbiolinks: TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data
Description
Usage
Arguments
Value
Examples
Description
This function is a auxiliary function to visualize GAIA output
(all significant aberrant regions.)
Usage
1
gaiaCNVplot(calls, threshold = 0.01)
Arguments
calls
A matrix with the following columns: Chromossome, Aberration Kind
Region Start, Region End, Region Size and score
threshold
Score threshold (orange horizontal line in the plot)
Value
A plot with all significant aberrant regions.
Examples
1
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call <- data.frame("Chromossome" = rep(9,100),
"Aberration Kind" = rep(c(-2,-1,0,1,2),20),
"Region Start [bp]" = 18259823:18259922,
"Region End [bp]" = 18259823:18259922,
"score" = rep(c(1,2,3,4),25))
gaiaCNVplot(call,threshold = 0.01)
call <- data.frame("Chromossome" = rep(c(1,9),50),
"Aberration Kind" = rep(c(-2,-1,0,1,2),20),
"Region Start [bp]" = 18259823:18259922,
"Region End [bp]" = 18259823:18259922,
"score" = rep(c(1,2,3,4),25))
gaiaCNVplot(call,threshold = 0.01)
daniel615212950/TCGAbiolinks documentation built on Dec. 19, 2021, 8:06 p.m.
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Description Usage Arguments Value Examples
Description
This function is a auxiliary function to visualize GAIA output (all significant aberrant regions.)
Usage
1 | gaiaCNVplot(calls, threshold = 0.01)
|
Arguments
calls |
A matrix with the following columns: Chromossome, Aberration Kind Region Start, Region End, Region Size and score |
threshold |
Score threshold (orange horizontal line in the plot) |
Value
A plot with all significant aberrant regions.
Examples
1 2 3 4 5 6 7 8 9 10 11 12 | call <- data.frame("Chromossome" = rep(9,100),
"Aberration Kind" = rep(c(-2,-1,0,1,2),20),
"Region Start [bp]" = 18259823:18259922,
"Region End [bp]" = 18259823:18259922,
"score" = rep(c(1,2,3,4),25))
gaiaCNVplot(call,threshold = 0.01)
call <- data.frame("Chromossome" = rep(c(1,9),50),
"Aberration Kind" = rep(c(-2,-1,0,1,2),20),
"Region Start [bp]" = 18259823:18259922,
"Region End [bp]" = 18259823:18259922,
"score" = rep(c(1,2,3,4),25))
gaiaCNVplot(call,threshold = 0.01)
|
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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