flowHC: Cluster cytometry data using hierarchical clustering
In hzc363/MetaCyto: MetaCyto: A package for meta-analysis of cytometry data
Description
Usage
Arguments
Value
Examples
Description
A function that cluster cytometry data using hierarchical clustering.
Usage
1
flowHC(fcsFrame, excludeClusterParameters, minimumClusterSizePercent = 0.05)
Arguments
fcsFrame
A flow frame.
excludeClusterParameters
A vector specifying the name of markers not
to be used for clustering.
minimumClusterSizePercent
A number between 0 and 1, used to specify
the minimum size of a cluster relative to all events.
Value
A list of clusters. Each cluster contains the ID of all cells that
belong to the cluster.
Examples
1
2
3
4
5
6
7
8
9
# Find fcs files
files=system.file("extdata","SDY420/ResultFiles/CyTOF_result",
package="MetaCyto")
files=list.files(files,pattern="fcs$",full.names=TRUE)
# Preprocess
fcs = preprocessing(fcsFiles=files,assay ="CyTOF",b=1/8)
# cluster using flowHC
cluster_list=flowHC(fcsFrame=fcs,
excludeClusterParameters=c("Time","Cell_length"))
hzc363/MetaCyto documentation built on July 27, 2020, 2:46 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Description Usage Arguments Value Examples
Description
A function that cluster cytometry data using hierarchical clustering.
Usage
1 | flowHC(fcsFrame, excludeClusterParameters, minimumClusterSizePercent = 0.05)
|
Arguments
fcsFrame |
A flow frame. |
excludeClusterParameters |
A vector specifying the name of markers not to be used for clustering. |
minimumClusterSizePercent |
A number between 0 and 1, used to specify the minimum size of a cluster relative to all events. |
Value
A list of clusters. Each cluster contains the ID of all cells that belong to the cluster.
Examples
1 2 3 4 5 6 7 8 9 | # Find fcs files
files=system.file("extdata","SDY420/ResultFiles/CyTOF_result",
package="MetaCyto")
files=list.files(files,pattern="fcs$",full.names=TRUE)
# Preprocess
fcs = preprocessing(fcsFiles=files,assay ="CyTOF",b=1/8)
# cluster using flowHC
cluster_list=flowHC(fcsFrame=fcs,
excludeClusterParameters=c("Time","Cell_length"))
|
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.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.