cluster_fcs_files_in_dir: Cluster all FCS files contained in a directory
In ParkerICI/grappolo: Feature generation from single-cell data

Cluster all FCS files contained in a directory

1	cluster_fcs_files_in_dir(wd, ...)

wd

The directory containing the FCS files

...

Arguments passed on to cluster_fcs_files

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

num.samples

Number of samples to be used for the CLARA algorithm (see cluster::clara)

output.dir

The name of the output directory, it will be created if it does not exist

asinh.cofactor

Cofactor for asinh transformation. If this is NULL no transformation is performed

negative.values

How to deal with negative values in the data. If this is NULL negative values are left as is. Otherwise two options are possible:

truncate: Negative values will be truncated (i.e. replaced with 0)
shift: The data will be shifted so that only quantile.prob of the values for each channel will be truncated to 0. This option is useful in cases where the range of data significantly extends in the negatives, for instance due to compensation.

quantile.prob

Only used if negative.value is set to shift. The quantile of measurements that are going to be truncated to 0. For instance if this is 0.05, the data will be shifted so that only 5 percent of the values are negative and will be truncated to 0

Returns the list of files that have been clustered

ParkerICI/grappolo documentation built on April 8, 2021, 11:03 a.m.