cytof_addToFCS: Add data to the original FCS files

In JinmiaoChenLab/cytofkit: cytofkit: an integrated mass cytometry data analysis pipeline

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

Value

New fcs files stored under analyzedFCSdir

JinmiaoChenLab/cytofkit documentation built on Dec. 20, 2020, 8:52 p.m.