new_scGPS_object: new_scGPS_object

In IMB-Computational-Genomics-Lab/scGPS: A complete analysis of single cell subpopulations, from identifying subpopulations to analysing their relationship (scGPS = single cell Global Predictions of Subpopulation)

Description

new_scGPS_object generates a scGPS object in the SingleCellExperiment class for use with the scGPS package. This object contains an expression matrix, associated metadata (cells, genes, clusters). The data are expected to be normalised counts.

Usage

new_scGPS_object(
  ExpressionMatrix = NULL,
  GeneMetadata = NULL,
  CellMetadata = NULL,
  LogMatrix = NULL
)

Arguments

ExpressionMatrix	An expression matrix in data.frame or matrix format. Rows should represent a transcript and its normalised counts, while columns should represent individual cells.
GeneMetadata	A data frame or vector containing gene identifiers used in the expression matrix. The first column should hold the gene identifiers you are using in the expression matrix. Other columns contain information about the genes, such as their corresponding ENSEMBL transcript identifiers.
CellMetadata	A data frame containing cell identifiers (usually barcodes) and an integer representing which batch they belong to. The column containing clustering information needs to be the first column in the CellMetadata dataframe If clustering information is not available, users can run CORE function and add the information to the scGPS before running scGPS prediction
LogMatrix	optional input for a log matrix of the data. If no log matrix is supplied one will be created for the object

Value

This function generates an scGPS object belonging to the SingleCellExperiment.

Author(s)

Quan Nguyen, 2018-04-06

See Also

SingleCellExperiment

Examples

day2 <- day_2_cardio_cell_sample
t <-new_scGPS_object(ExpressionMatrix = day2$dat2_counts, 
    GeneMetadata = day2$dat2geneInfo, CellMetadata = day2$dat2_clusters)
colData(t); show(t); colnames(t)

IMB-Computational-Genomics-Lab/scGPS documentation built on Dec. 6, 2020, 3:20 p.m.