Description Usage Arguments Details Value
Cluster individual FCS files, using multiple CPU cores if possible
1 2 3 4 5 6 7 8 9 10 11 | cluster_fcs_files(
files.list,
num.cores,
col.names,
num.clusters,
asinh.cofactor,
num.samples = 50,
output.dir = ".",
negative.values = "truncate",
quantile.prob = 0.05
)
|
files.list |
The files to cluster |
num.cores |
Number of CPU cores to use |
col.names |
A vector of column names indicating which columns should be used for clustering |
num.clusters |
The desired number of clusters |
asinh.cofactor |
Cofactor for |
num.samples |
Number of samples to be used for the CLARA algorithm (see |
output.dir |
The name of the output directory, it will be created if it does not exist |
negative.values |
How to deal with negative values in the data. If this is
|
quantile.prob |
Only used if |
This function can produce two types of output:
"file"
: Two files will be written, with names derived by appending ".clustered.txt"
and
".all_events.rds"
to the file names in files.list
. The ".clustered.txt"
file is a tab-separated
table of median values for each cluster. The ".all_events.rds"
file is an RDS file (readable with base::readRDS
)
containing a data.frame
with all the rows in the original input file and an additional column called
cellType
, indicating cluster membership.
"directory"
: In addition to the ".clustered.txt"
file described above, this mode will create a folder
called "clusters_data"
. This folder will contain a sub-folder for each input file, containing separate RDS files
with the data in each cluster
Returns either NULL
or a try-error
object if some error occurred during the computation
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