cytof_addToFCS: Add data to the original FCS files
In JinmiaoChenLab/cytofkit2: cytofkit2: an integrated mass cytometry data analysis pipeline. Cytofkit provides functions for data pre-processing, fast clustering, data visualization through linear or non-linear dimensionality reduction, automatic identification of cell subsets, and inference of the relatedness between cell subsets

cytof_addToFCS

R Documentation

Add data to the original FCS files

Description

Store the new dimension transformed data and cluster data into the exprs matrix in new fcs files under analyzedFCSdir

Usage

cytof_addToFCS(
  data,
  rawFCSdir,
  origSampNames = NULL,
  analyzedFCSdir,
  transformed_cols = c("tsne_1", "tsne_2"),
  cluster_cols = c("cluster"),
  clusterIDs = NULL,
  specifySampleNames = NULL,
  inLgclTrans = TRUE
)

Arguments

`data`	The new data matrix to be added in.
`rawFCSdir`	The directory containing the original fcs files.
`origSampNames`	Vector of original names of samples, if samples were renamed.
`analyzedFCSdir`	The directory to store the new fcs files.
`transformed_cols`	The column name of the dimension transformed data in `data`.
`cluster_cols`	The column name of the cluster data in `data`.
`clusterIDs`	Table of cell cluster IDs for each clustering method
`specifySampleNames`	Used only if sample names differ from those in raw fcs.
`inLgclTrans`	If `TRUE`, apply the inverse lgcl transformation to the the cluster data before saving