dafsFilter: dafsFilter Function to filter expression data within an "se"...
In avastermark19/doseR_0.99.7: doseR
Description
Usage
Arguments
Details
Value
Author(s)
References
Examples
Description
This function filters the expression of the supplied
"se" object, by invoking the dafsFilter (dafs) function. dafsFilter is a
filtering function used to remove rows (genes) of various expression data.
Usage
1
dafsFilter(se, PLOT=TRUE)
Arguments
se
A SummExp object.
PLOT
Boolean, toggles plotting.
Details
This function filters the expression of the supplied se object
using a Data Adaptive Flag filter. The internal function uses a vector
to store Kolmogorov Smirnov distance statistics, loops through cuts of
the data to determine targeted K-S statistic, selects data greater than
a quantile and runs Mclust on that data to determine theoretical
distribution. The wrapper uses simpleFilter to determine first left-most
local minima (using the Earth library).
Value
Returns an invisible, filtered SummExp object.
Author(s)
AJ Vaestermark, JR Walters.
References
BMC Bioinformatics, 2014, 15:92
Examples
1
2
3
4
library(mclust)
library(edgeR)
data(hmel.se)
f_se <- dafsFilter(se)
avastermark19/doseR_0.99.7 documentation built on May 29, 2019, 8:30 a.m.
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Description Usage Arguments Details Value Author(s) References Examples
Description
This function filters the expression of the supplied "se" object, by invoking the dafsFilter (dafs) function. dafsFilter is a filtering function used to remove rows (genes) of various expression data.
Usage
1 | dafsFilter(se, PLOT=TRUE)
|
Arguments
se |
A SummExp object. |
PLOT |
Boolean, toggles plotting. |
Details
This function filters the expression of the supplied se object using a Data Adaptive Flag filter. The internal function uses a vector to store Kolmogorov Smirnov distance statistics, loops through cuts of the data to determine targeted K-S statistic, selects data greater than a quantile and runs Mclust on that data to determine theoretical distribution. The wrapper uses simpleFilter to determine first left-most local minima (using the Earth library).
Value
Returns an invisible, filtered SummExp object.
Author(s)
AJ Vaestermark, JR Walters.
References
BMC Bioinformatics, 2014, 15:92
Examples
1 2 3 4 | library(mclust)
library(edgeR)
data(hmel.se)
f_se <- dafsFilter(se)
|
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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