cluster_fcs_files_groups: Pool FCS files and cluster them

Description Usage Arguments Value

View source: R/cluster.R

Description

Pool FCS files and cluster them

Usage

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cluster_fcs_files_groups(files.list, num.cores, col.names, num.clusters,
  asinh.cofactor, num.samples = 50, downsample.to = 0,
  output.dir = ".", negative.values = "truncate",
  quantile.prob = 0.05)

Arguments

files.list

A named list of vectors detailing how the files should be pooled before clustering. Files in the same vector will be pooled together. The name of the output is going to correspond to the name of the corresponding list element.

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 asinh transformation. If this is NULL no transformation is performed

num.samples

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

downsample.to

The number of events that should be randomly sampled from each file before pooling. If this is 0, no sampling is performed

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 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

Value

Returns either NULL or a try-error object if some error occurred during the computation


ParkerICI/scfeatures documentation built on Aug. 2, 2019, 1:44 a.m.