cytof_addToFCS: Add data to the original FCS files

Description Usage Arguments Value

View source: R/cytof_postProcess.R

Description

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

Usage

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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


cytofkit documentation built on Nov. 17, 2017, 9:25 a.m.