Clean_Up_Input: Clean Up Input

In EDePasquale/DoubletDecon: A Package to Identify Doublets and Doublet Clusters Based on Deconvolution Analysis and Unique Gene Expression

Description

This function cleans up the raw data and groups files. It replaces the column clusters in the expression file with the clusters in the groups file. It ensures that all expression files have a column_clusters-flat and row_clusters-flat (even when data not provided it adds NAs). It uses Renumber as necessary to avoid non-consecutive cluster identifications.

Usage

Clean_Up_Input(rawData, groups, rowClusters = NULL, log_file_name)

Arguments

rawData	ICGS expression or counts file (in ICGS expression file format).
groups	ICGS groups file.
rowClusters	Optional vector containing row cluster information (used by Recluster). Default is NULL.
log_file_name	used for saving run notes to log file

Value

processed - data.frame of genes by samples with a row of cell clusters (column_clusters-flat) and a column of gene clusters (row_clusters-flat) when available.

groups - groups file with cell names matching the expression file.

EDePasquale/DoubletDecon documentation built on Dec. 3, 2020, 10:44 p.m.